[Federal Register Volume 86, Number 100 (Wednesday, May 26, 2021)]
[Proposed Rules]
[Pages 28301-28323]
From the Federal Register Online via the Government Publishing Office [www.gpo.gov]
[FR Doc No: 2021-10421]
[[Page 28301]]
=======================================================================
-----------------------------------------------------------------------
DEPARTMENT OF COMMERCE
Patent and Trademark Office
37 CFR Part 1
[Docket No. PTO-P-2020-0032]
RIN 0651-AD48
Electronic Submission of a Sequence Listing, a Large Table, or a
Computer Program Listing Appendix in Patent Applications
AGENCY: United States Patent and Trademark Office, Department of
Commerce.
ACTION: Notice of proposed rulemaking.
-----------------------------------------------------------------------
SUMMARY: The United States Patent and Trademark Office (USPTO or
Office) proposes to amend the rules of practice to permit higher-
capacity physical media to be submitted to the USPTO. Patent
applications for certain inventions require significant data in
American Standard Code for Information Interchange (ASCII) text format
to be submitted to the USPTO in order to determine whether the
invention described in the patent application is patentable. When
submission of such data exceeds the USPTO's patent electronic filing
system capacity, direct submission would not be possible for a large
data submission in ASCII text format. To that end, the rules of
practice are proposed to be amended to provide applicants with the
ability to use physical media larger than compact discs (CDs) for
submission of an electronic version of amino acid and nucleotide
sequence information, information compiled in a large table, and
information relating to a computer program listing. Additionally,
changes regarding extraction of compressed data files, which had not
been permitted in the past for certain submissions, would be permitted
if compliant with the requirements of the proposed rules. Other rules
relating to certain obsolete and non-secure methods of presenting data
would be eliminated.
DATES: Comments must be received by July 26, 2021 to ensure
consideration.
ADDRESSES: For reasons of Government efficiency, comments must be
submitted through the Federal eRulemaking Portal at
www.regulations.gov. To submit comments via www.regulations.gov, enter
docket number PTO-P-2020-0032 on the homepage and click ``Search.'' The
site will provide a search results page listing all documents
associated with this docket. Find a reference to this document and
click on the ``Comment Now!'' icon, complete the required fields, and
enter or attach your comments. Attachments to electronic comments will
be accepted in ADOBE[supreg] portable document format or MICROSOFT
WORD[supreg] format. Because comments will be made available for public
inspection, information that the submitter does not desire to make
public, such as an address or phone number, should not be included in
the comments.
Visit the Federal eRulemaking Portal website (www.regulations.gov)
for additional instructions on providing comments via the portal. If
electronic submission of comments is not feasible due to lack of access
to a computer and/or the internet, please contact the USPTO using the
contact information below for special instructions.
FOR FURTHER INFORMATION CONTACT: Mary C. Till, Senior Legal Advisor,
Office of Patent Legal Administration, Office of the Deputy
Commissioner for Patents, by email at [email protected]; or Ali
Salimi, Senior Legal Advisor, Office of Patent Legal Administration,
Office of the Deputy Commissioner for Patents, by email at
[email protected]. Contact via telephone at 571-272-7704 if further
instruction is needed for the submission of comments.
SUPPLEMENTARY INFORMATION:
Background: In order to permit the submission of large amounts of
data in patent applications where such a submission exceeds the
capacity for filing via the USPTO patent electronic filing systems,
this rulemaking seeks to expand the types of physical media that can be
used for such a submission. The volume of applications in which such
large amounts of data may need to be submitted is a small fraction of
the total number of applications that the USPTO receives every year.
Expanding the types of physical media that can be used by these
applicants achieves the intent with minimal changes to the USPTO's
processing of such large amounts of data.
With respect to the submission of data relating to biotechnology
inventions, the proposed rules would no longer permit an applicant to
rely on a previously submitted computer readable form (CRF) of required
sequence information. The proposed rules thus ensure the robustness of
the data by requiring the applicant to confirm that the data presented
is the correct information for the examiner to consider during the
examination process. Since the proposed rules will also permit an ASCII
plain text file to serve as both the sequence listing itself and the
CRF of the sequence listing, these changes are expected to have a
minimal impact on applicants in general.
The USPTO encourages applicants to file their patent applications
via its USPTO patent electronic filing system and imposes a surcharge
for non-electronic filing of an original patent application (excluding
reissue, design, plant, and provisional applications), as mandated by
section 10(h) of Public Law 112-29, September 16, 2011 (Leahy-Smith
America Invents Act). The USPTO provides information (Legal Framework
for Patent Electronic System) concerning electronic filing via the
USPTO patent electronic filing system on its website at www.uspto.gov/patents-application-process/filing-online/legal-framework-efs-web and
in section 502.05 of the Manual of Patent Examining Procedure (MPEP,
Ninth Edition, Revision 10.2019). In particular, the USPTO patent
electronic filing system permits submission of ASCII plain text files
(.txt) for submission of a ``Sequence Listing,'' a CRF of a ``Sequence
Listing,'' ``Large Tables,'' and a ``Computer Program Listing
Appendix.'' Although a USPTO patent electronic filing system submission
of such ASCII plain text files is preferred, it is possible that the
system limitations of the USPTO patent electronic filing system may not
accommodate large ASCII text files. Currently, in those circumstances,
such text files may be submitted on compact disc under 37 CFR 1.52(e),
and images of such text files may be submitted in Portable Document
Format (PDF) via the USPTO patent electronic filing system (except for
a CRF of a ``Sequence Listing'' or a ``Computer Program Listing
Appendix'' having over 300 lines--these must be submitted on compact
disc under 37 CFR 1.52(e)). The proposed changes to the rules of
practice pertaining to a ``Sequence Listing,'' a CRF of a ``Sequence
Listing,'' ``Large Tables,'' and a ``Computer Program Listing
Appendix'' would harmonize the rules for filing such documents in
electronic form with the requirements and conditions set forth in the
Legal Framework for Patent Electronic System. The proposed changes do
not alter the requirements and conditions set forth in the Legal
Framework for Patent Electronic System.
Submission of ASCII plain text files: Currently, electronic
documents in ASCII file format that are to become part of the permanent
USPTO records in the file of a patent application, reexamination, or
supplemental examination proceeding that exceed the USPTO patent
electronic filing system limits may be submitted on a compact disc. Due
to the limited storage capacity
[[Page 28302]]
of compact discs, the USPTO is proposing revisions to permit use of
Digital Video Disc-Recordable (DVD-R or DVD+R). These higher-capacity
read-only optical discs, on which data is permanently recorded and
cannot be changed or erased, significantly reduce the number of
physical media required to accommodate large files.
In the case of a ``Sequence Listing,'' MPEP section 2422.03
indicates that if a new application is filed via the USPTO patent
electronic filing system with an ASCII plain text file of a ``Sequence
Listing'' that complies with the requirements of 37 CFR 1.824(a)(2)
through (6) and (b), and the applicant has not filed a ``Sequence
Listing'' in a PDF image file, the text file will serve as both the
paper copy required by 37 CFR 1.821(c) and the CRF required by 37 CFR
1.821(e). This concept is expressly incorporated into these proposed
changes to the rules of practice. The current size limitation for an
ASCII plain text file of a ``Sequence Listing'' submitted via the USPTO
patent electronic filing system is 100 megabytes (MB). Thus, if an
applicant files an ASCII plain text file of a ``Sequence Listing'' that
is 100 MB or less, that ASCII plain text file serves as both the
``Sequence Listing'' under 37 CFR 1.821(c) and the CRF of the
``Sequence Listing'' under 37 CFR 1.821(e). With respect to ``Large
Tables'' and a ``Computer Program Listing Appendix,'' if ASCII plain
text files are filed through the USPTO patent electronic filing system,
then no separate submission of disc copies of ASCII plain text files
are needed. However, the current system limit of ASCII plain text file
submissions of ``Large Tables'' and a ``Computer Program Listing
Appendix'' is 25 MB per submission. This limit, however, may not
prevent an entirely electronic submission. According to the Legal
Framework for Patent Electronic System, cited supra, a user may be able
to break up a ``Computer Program Listing Appendix'' or ``Large Tables''
file that is larger than 25 MB into multiple files that are no larger
than 25 MB each and submit those smaller files via the USPTO patent
electronic filing system. If the user chooses to break up a large
``Computer Program Listing Appendix'' or ``Large Tables'' file so it
may be submitted electronically, the file names must indicate their
order (e.g., ``1 of X,'' ``2 of X''). Files above the 25 MB limit for
``Large Tables'' and a ``Computer Program Listing Appendix'' (unless
capable of being divided) and above 100 MB for a ``Sequence Listing''
will have to be submitted on read-only optical discs. Submission of a
``Sequence Listing'' as an ASCII text file, if it exceeds 100 MB,
cannot be divided like a submission of a ``Large Table'' or a
``Computer Program Listing Appendix.'' Thus, any ``Sequence Listing''
greater than 100 MB must be submitted on read-only optical discs.
Currently, such files cannot be compressed; this can necessitate the
use of multiple CD-ROMs or CD-Rs. These proposed changes to the rules
of practice will permit higher-capacity media as well as non-self-
extracting file compression. By permitting file compression, material
submitted on a read-only optical disc will be capable of fitting on a
single disc with the data integrity remaining intact.
The current rules of practice (37 CFR 1.52(e), 1.96(c), and 1.824)
recite the use of certain obsolete computer and operating system
formats. Updated computer and operating system formats are proposed to
be added, and reference to obsolete media will be eliminated. Proposed
changes to 37 CFR 1.58 will recite the updated computer and operating
system compatibilities.
When a patent application relies on subject matter from an ASCII
plain text file submitted on physical media or via the USPTO patent
electronic filing system, currently, the patent specification must
contain an incorporation by reference statement pursuant to 37 CFR
1.77(b)(5) or the Legal Framework for Patent Electronic System. The
rules relating to the arrangement of the specification are proposed to
be amended to clarify the required incorporation by reference
statement. The granted patent or pre-grant publication of an
application that includes an ASCII plain text file, whether submitted
on optical read-only discs or via the USPTO patent electronic filing
system, does not include the actual contents of the ASCII plain text
file in the printed document. The incorporation by reference is
necessary to treat the material in the ASCII file as part of the patent
or publication and to alert the public that the granted patent or the
pre-grant publication includes additional material that constitutes
part of the patent or publication. Although the current rules and
proposed changes to the rules of practice permit a cross-reference to
related applications to be included in the specification, in accordance
with 37 CFR 1.76, it should be noted that the USPTO does not recognize
a benefit or priority claim presented only in the specification for
patent applications filed on or after September 16, 2012. For these
applications or patents issued from such applications, a benefit claim
(37 CFR 1.78) or priority claim (37 CFR 1.55) must be presented on an
Application Data Sheet for an original application in order to be
recognized by the USPTO.
Sequence Listings: Any patent application that contains unbranched
nucleotide sequences with 10 or more nucleotide bases or unbranched,
non-D amino acid sequences with 4 or more amino acids, provided that
there are at least 10 ``specifically defined'' nucleotides or 4
``specifically defined'' amino acids, must contain a ``Sequence
Listing'' and a CRF of the ``Sequence Listing.'' Under the current
rules, a ``Sequence Listing'' exceeding the USPTO patent electronic
filing system submission limit must be submitted with a total of three
disc copies to the USPTO to comply with the ``Sequence Listing''
regulation requirements. The three disc copies are (1) a first disc
copy of ASCII plain text file on a compact disc to comply with 37 CFR
1.821(c), (2) a second identical disc copy of the ASCII plain text file
on compact disc to comply with the duplicate submission requirement in
37 CFR 1.52(e)(4) when submitting the 37 CFR 1.821(c) sequence listing,
and (3) a CRF copy of the ASCII plain text file on compact disc,
identical to the 37 CFR 1.821(c) submission. The proposed rule changes
would permit that a single read-only optical disc copy of a ``Sequence
Listing'' as an ASCII plain text file could be submitted, and that such
submission would comply with both the listing requirement (37 CFR
1.821(c)) and the CRF requirement (37 CFR 1.821(e)). For submission via
the USPTO patent electronic filing system, the ASCII plain text file,
not the PDF version, would serve to comply with both 37 CFR 1.821(c)
and 1.821(e). The following table summarizes the mechanics of
submitting a ``Sequence Listing'' under the proposed changes to the
rules of practice in applications, except for international
applications during the international stage, based on the current USPTO
patent electronic filing system limit of 100 MB for an ASCII plain text
file and a system limit of 25 MB for PDF files.
[[Page 28303]]
----------------------------------------------------------------------------------------------------------------
Surcharge under 37
CFR 1.21(o) for
Preferred Acceptable Specification submission of a
Size of ``Sequence Listing'' submission submission statement ``Sequence
requirements Listing'' in
electronic form
----------------------------------------------------------------------------------------------------------------
100 MB or less.................. ASCII plain text The ``Sequence Incorporation by None.
file submitted Listing'' in reference of the
via the USPTO physical paper ASCII text file
patent electronic copies or into the
filing system, submitted via the specification
complies with USPTO patent (see MPEP 502.05).
both 37 CFR electronic filing
1.821(c) and system as a PDF
1.821(e), no image file and a
separate CRF CRF on a read-
needed. only optical disc
along with a
statement that
the CRF and the
physical paper/
PDF image file
submission are
the same.
101 MB to 299 MB................ ASCII plain text The ``Sequence Incorporation by None.
file submitted on Listing'' in reference of the
a read-only physical paper ASCII text file
optical disc in a copies and a CRF into the
single copy, the on a read-only specification (37
single copy optical disc CFR 1.52(e)(8)).
complies with along with a
both 37 CFR statement that
1.821(c) and the CRF and the
1.821(e), no physical paper
separate CRF submission are
needed. the same.
300 MB to 799 MB................ ASCII plain text The ``Sequence Incorporation by 37 CFR 1.21(o)(1):
file submitted on Listing'' in reference of the Currently $1,000
a read-only physical paper ASCII text file for an
optical disc in a copies and a CRF into the undiscounted
single copy, the on a read-only specification (37 entity, $500 for
single copy optical disc CFR 1.52(e)(8)). a small entity,
complies with along with and $250 for a
both 37 CFR statement that micro entity.
1.821(c) and the CRF and the
1.821(e), no physical paper
separate CRF submission are
needed. the same.
800 MB or above................. ASCII plain text The ``Sequence Incorporation by 37 CFR 1.21(o)(2):
file submitted on Listing'' in reference of the Currently $10,000
a read-only physical paper ASCII text file for an
optical disc in a copies and a CRF into the undiscounted
single copy, the on a read-only specification (37 entity, $5,000
single copy optical disc CFR 1.52(e)(8) as for a small
complies with along with a added in these entity, and
both 37 CFR statement that proposed rules). $2,500 for a
1.821(c) and the CRF and the micro entity.
1.821(e), no physical paper
separate CRF submission are
needed. Should the same.
more than one
disc be needed,
then only a
single copy of
the additional
disc(s) would be
needed, no
additional CRF
needed since the
read-only optical
discs (if
multiple are
needed) need NOT
be submitted in
duplicate.
----------------------------------------------------------------------------------------------------------------
The current rules of practice relating to form, content, and
submission requirements of ``Sequence Listings'' comply with World
Intellectual Property Organization (WIPO) Standard ST.25. In this
document, the proposed rule changes and modifications also conform to
WIPO Standard ST.25.
To simplify and streamline the processing of patent applications
with sequences of amino acids and nucleotides as defined in 37 CFR
1.821(a), submission of a ``Sequence Listing'' in ASCII plain text file
format, either directly via the USPTO patent electronic filing system
or on a read-only optical disc, will be sufficient to comply with the
listing requirement and the CRF requirement (37 CFR 1.821(c) and
1.821(e)). That is, if a ``Sequence Listing'' in ASCII plain text file
format is filed either directly via the USPTO patent electronic filing
system or on a read-only optical disc, then no additional CRF copy will
be needed. In such a situation, an incorporation by reference statement
in the specification, in accordance with 37 CFR 1.77(b)(5), would still
be required, except such a statement will not be required in an
international application during the international stage. As with the
current rules, the proposed changes continue to permit submission of a
``Sequence Listing'' on physical sheets of paper or as a PDF image
file. Furthermore, like the current rules, the proposed rules will
require payment of the application size fee (37 CFR 1.16(s)) for
physical sheets of paper of a ``Sequence Listing'' or a PDF of a
``Sequence Listing'' that results in an application size that exceeds
100 sheets of paper. Submission of the ``Sequence Listing'' as a PDF or
on physical sheets of paper would still require a separate CRF of the
``Sequence Listing.'' Similarly, should the ASCII plain text file of
the ``Sequence Listing'' exceed the system limits of the USPTO patent
electronic filing system (currently at 100 MB), then a single copy of
an ASCII plain text file of the ``Sequence Listing'' submitted on a
read-only optical disc would not require a separate electronic copy of
a CRF of the ``Sequence Listing.'' In circumstances in which a separate
CRF is filed, the statement, in accordance with 37 CFR
1.821(e)(2)(iii), that the CRF is identical to either the PDF or the
physical paper version of the ``Sequence Listing'' is required.
The proposed rule changes will no longer permit the transfer of a
CRF from a parent or related application to the newly filed original
application. In light of the availability to download a ``Sequence
Listing'' from granted U.S. patents and U.S. patent application
publications via Public PAIR in the Supplemental Content tab, there is
no longer a need for a CRF transfer. Such electronic copies of a
``Sequence Listing'' may also be available on another intellectual
property office's website or on the WIPO--PATENTSCOPE website. In the
extremely rare circumstance in which the ``Sequence Listing'' exceeds
the download capability (currently 650 MB), then a request for the
content of a granted U.S. patent or U.S. patent application publication
(including the ``Sequence Listing'' submitted on disc) can be made to
the Patent and Trademark Copy Fulfillment Branch. Therefore, these
proposed changes to the rules of practice will eliminate the practice
of CRF transfers.
WIPO Standard ST.26 is expected to take effect on January 1, 2022,
and will replace WIPO Standard ST.25. WIPO Standard ST.26 will require
that a
[[Page 28304]]
``Sequence Listing'' must be presented as a single file in eXtensible
Markup Language (XML). As a result, in an original application filed on
or after January 1, 2022, the ``Sequence Listing'' part will not be
accepted on physical sheets of paper or as a PDF image file. Therefore,
to prepare for the changes under WIPO Standard ST.26, the USPTO is
proposing to revise the rules of practice to facilitate ``Sequence
Listing'' submissions by requiring a single ASCII plain text file
submission that would both meet the ``Sequence Listing'' requirement
and serve as the CRF of the ``Sequence Listing.'' That is, under these
proposed rule changes, a single ASCII plain text file submission of a
``Sequence Listing'' would comply with both 37 CFR 1.821(c) and (e).
Currently, 37 CFR 1.821(a) incorporates by reference six tables
from Appendix 2 of WIPO Standard ST.25 that provide the nucleotide and
amino acid symbols and feature tables. For convenience, a further
proposed modification of the ``Sequence Listing'' rules involves adding
these tables as Appendices A-F of Subpart G of Part 1 (explicitly
incorporating the text of the WIPO tables into the CFR). Currently, 37
CFR 1.823(b) includes a table containing all numeric identifiers. To
improve the readability of the regulations, this table is proposed to
be moved to Appendix G.
Updates to amendment practice for ``Large Tables,'' a ``Computer
Program Listing Appendix,'' and ``Sequence Listings'': In general, the
manner of making amendments in applications requires that the text of
any added subject matter must be shown by underlining the added text
and that the text of any deleted matter must be shown by strike-
through. However, computer listings (37 CFR 1.96) and ``Sequence
Listings'' (37 CFR 1.825) are currently exempted from these general
requirements (37 CFR 1.121(b)). These proposed changes to the rules of
practice will require a description of the amendments made in ``Large
Tables,'' a ``Computer Program Listing Appendix,'' and ``Sequence
Listings'' to more easily and accurately identify any changes made to
the information contained in such submissions (37 CFR 1.121(b)(6)).
This proposed rule includes requirements for amendments to an ASCII
plain text file containing ``Large Tables'' (37 CFR 1.58(g)) or a
``Computer Program Listing Appendix'' (37 CFR 1.96(c)(5)(i)) that are
accomplished by a replacement of an ASCII plain text file. Providing a
replacement may be required if, for example, the information on the
disc is corrupted. A replacement ASCII plain text file must be
submitted, either via the USPTO patent electronic filing system or on a
read-only optical disc, together with an incorporation by reference of
the material in the replacement ASCII plain text file in a separate
paragraph of the specification; a statement that identifies the
location of all deletions, replacements, or additions to the ASCII
plain text file; and a statement that the replacement ASCII plain text
file contains no new matter.
Discussion of Specific Rules
Section 1.52: The heading of Sec. 1.52 is proposed to read:
Language, paper, writing, margins, read-only optical disc
specifications.
Section 1.52(e) is proposed to be amended to reference electronic
documents ``submitted on a read-only optical disc,'' with additional
conforming changes made throughout. Currently, Sec. 1.52(e) references
``electronic documents'' that are to become part of the USPTO records
in patent applications, reexaminations, and supplemental examination
proceedings. Since Sec. 1.52(e) only governs electronic documents
submitted on discs, in particular as proposed, read-only optical discs,
the heading is more specific to the types of electronic documents
covered by the regulation.
Section 1.52(e)(1) is proposed to be updated to specifically refer
to a ``Computer Program Listing Appendix,'' as provided for in Sec.
1.96(c), and to require that the ``Sequence Listing'' on a read-only
optical disc submitted under Sec. 1.821(c) must be in compliance with
Sec. 1.824. Section 1.52(e)(1) is proposed to be revised to indicate
that ``Large Tables,'' as described in the proposed changes to Sec.
1.58(c), may be submitted on a read-only optical disc to become part of
the permanent USPTO record.
Section 1.52(e)(2) is proposed to be revised to replace ``compact''
with ``read-only optical'' and to incorporate conformity to the
International Organization for Standardization (ISO) 9660 standard,
which was previously located in Sec. 1.52(e)(3). Additionally, Sec.
1.52(e)(2) maintains the availability of CD-ROM and CD-R as options for
physical media (Sec. 1.52(e)(2)(i)) but also expands the types of
media options to include Digital Video Disc-Recordable (DVD-R or DVD+R)
(Sec. 1.52(e)(2)(ii)).
Section 1.52(e)(3) is proposed to be reorganized for improved
readability. The computer compatibility (Sec. 1.52(e)(3)(i)) and
operating system compatibility (Sec. 1.52(e)(3)(ii)) are expressly
provided. Furthermore, the proposed changes to the rules of practice
indicate the use of ASCII plain text is required when submitting files
on physical media (Sec. 1.52(e)(3)(iii)). The proposed changes would
permit file compression for ASCII plain text files, which must be done
in accordance with Sec. Sec. 1.58, 1.96, and 1.824, as applicable
(Sec. 1.52(e)(3)(iii)).
Section 1.52(e)(4) is proposed to be revised to eliminate its
requirements for a duplicate copy and accompanying statement that the
two discs are identical. References to ``Copy 1'' and ``Copy 2'' are
deleted, and references to ``compact disc'' are updated to ``read-only
optical disc.'' However, duplicate copies of read-only optical discs
for ``Large Tables'' or a ``Computer Program Listing Appendix'' will
still be required, and Sec. Sec. 1.58 and 1.96 are proposed to be
amended to provide for such duplicate copies. Duplicate copies for
``Large Tables'' and a ``Computer Program Listing Appendix'' would
still be required to be submitted since the Office of Patent
Application Processing (OPAP) keeps a first copy for record retention
purposes and a second copy in an artifact folder for use by the
examiner during the patent examination process. A ``Sequence Listing,''
however, is not processed in the same manner. Accordingly, only a
single copy of a read-only optical disc containing the ``Sequence
Listing'' in ASCII plain text is needed, as such copy will serve as
both the listing as required by 37 CFR 1.821(c) and the CRF copy as
required by 37 CFR 1.821(e). Section 1.52(e)(4) is also proposed to
require that the read-only optical discs are enclosed in a hard case
within an unsealed, padded, and protective mailing envelope and that
such submission is accompanied by a transmittal letter. The information
regarding the read-only optical disc to be included in the transmittal
letter is expressly enumerated in items (i)-(vi) of this rule.
Section 1.52(e)(5) is proposed to be revised to enumerate the
labeling requirements of the read-only optical disc that had previously
been enumerated in Sec. 1.52(e)(6). The incorporation by reference
found in the current Sec. 1.52(e)(5) is deleted and moved to Sec.
1.52(e)(8).
Section 1.52(e)(6) is proposed to be revised to state that the
read-only optical discs may not be retained as part of the patent
application file and will not be returned to the applicant. The current
USPTO processing of compact discs would equally apply to read-only
optical discs. For ``Large Tables'' or a ``Computer Program Listing
Appendix,'' the process involves the OPAP receiving the read-only
optical discs, creating an artifact sheet for inclusion in the Image
File Wrapper, and reviewing the ASCII plain text file. Under the
current rules, a first copy of the read-only optical disc
[[Page 28305]]
is kept for record retention purposes, and a second copy is maintained
in an artifact folder for use by the examiner during the patent
examination process. For a ``Sequence Listing,'' the proposal would
require the submission of a single read-only optical disc. Once the
``Sequence Listing'' is loaded into the USPTO's Supplemental Complex
Repository for Examiners (SCORE) system, the physical media may be
retained by the Patent Legal Research Center. A ``Sequence Listing''
from granted U.S. patents and U.S. patent application publications is
available via Public PAIR in the Supplemental Content tab. Such
electronic copies of a ``Sequence Listing'' may also be available on
another intellectual property office's website, or on the WIPO--
PATENTSCOPE website. In the extremely rare circumstance in which the
``Sequence Listing'' exceeds the download capability (currently 650
MB), then a request for the content of a granted U.S. Patent or U.S.
patent application publication (including the ``Sequence Listing''
submitted on disc) can be made to the Patent and Trademark Copy
Fulfillment Branch.
Section 1.52(e)(7) is proposed to be revised to state that any
amendment to the information on a read-only optical disc must be made
in accordance with specified provisions, specifically, in compliance
with Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5) for a
``Computer Program Listing Appendix,'' and Sec. 1.825(b) for a
``Sequence Listing'' or a CRF of a ``Sequence Listing.''
Section 1.52(e)(8) is proposed to be added to state that the
specification must contain an incorporation by reference (Sec.
1.77(b)(5)) of the material contained on each read-only optical disc in
a separate paragraph, except for an international application in the
international stage. Additionally, the USPTO may require the applicant
to amend the specification to include the material incorporated by
reference.
Section 1.52(e)(9) is proposed to be added to indicate that should
a file be unreadable, then the USPTO will treat the submission as not
ever having been submitted. A file is unreadable if, for example, it is
of a format that does not comply with the requirements of Sec.
1.52(e)(2), it is corrupted, or it is written onto a defective read-
only optical disc. In such a case, OPAP will issue a notice indicating
that the file is unreadable, and a replacement will be required.
Section 1.52(f) is proposed to be amended to include the subtitle
``Determining application size fees for applications containing
electronic documents submitted on a read-only optical disc or via the
USPTO patent electronic filing system.''
Section 1.52(f)(1) is proposed to be amended to clarify the
determination of application size fees for application components
submitted on a read-only optical disc in compliance with Sec. 1.52(e),
where an electronic form of any ``Sequence Listing,'' in compliance
with either Sec. 1.821(c) or (e), and any ``Computer Program Listing
Appendix,'' in compliance with Sec. 1.96(c), are specifically excluded
from the application size fee determination. As stated in 35 U.S.C.
41(a)(1)(G), ``any sequence listing'' or a ``computer program listing''
submitted in electronic form is expressly excluded from any application
size fee calculation. A ``Computer Program Listing Appendix'' is
considered a ``computer program listing.''
Section 1.52(f)(2) is proposed to be amended to clarify the
determination of application size fees for applications submitted in
whole or in part via the USPTO patent electronic filing system and also
to clarify that any electronic form of a ``Sequence Listing,'' in
compliance with either Sec. 1.821(c) or (e), and any ``Computer
Program Listing Appendix,'' in compliance with Sec. 1.96(c), are
specifically excluded from the application size fee determination. As
stated in 35 U.S.C. 41(a)(1)(G), ``any sequence listing'' or a
``computer program listing'' submitted in electronic form is expressly
excluded from any application size fee calculation. A ``Computer
Program Listing Appendix'' is considered a ``computer program
listing.''
Section 1.52(f)(3) is proposed to be added to provide a surcharge
for submission of a ``Sequence Listing'' in electronic form in an
application under 35 U.S.C. 111 or 371 that is 300 MB or larger in
size. The lengthy ``Sequence Listing'' surcharge is set forth in Sec.
1.21(o). This means that a ``Sequence Listing'' submitted in electronic
form on read-only optical discs in compliance with either Sec. Sec.
1.821(c) either/or 1.821(e) that is 300 MB or larger in size will incur
a surcharge under Sec. 1.21(o). When the electronic form of the
``Sequence Listing'' is between 300 MB and 800 MB, a surcharge under
Sec. 1.21(o)(1) will be required. If the electronic form of the
``Sequence Listing'' exceeds 800 MB, then a surcharge under Sec.
1.21(o)(2) will be imposed.
Section 1.58: Section 1.58(b) is proposed to delete references to
Sec. Sec. 1.96(c) and 1.821(c) regarding tables submitted in
electronic form and to set forth format requirements, from former Sec.
1.58(c), that apply generally to chemical and mathematical formulas and
tables.
Section 1.58(c) is proposed to be rewritten to define ``Large
Tables'' that may be submitted in electronic form in ASCII plain text
via the USPTO patent electronic filing system or on a read-only optical
disc, in compliance with Sec. 1.52(e), excluding an international
application during the international stage. Additionally, the current
USPTO processing of ``Large Tables'' submitted on a read-only optical
disc involves a first copy, for record retention purposes, and a second
copy, for use during the examination process.
Section 1.58(d) is proposed to be added to list the format
requirements of ``Large Tables'' submitted in electronic form in ASCII
plain text. The format requirements address the spatial relationship of
table elements, computer compatibility, operating system compatibility,
the use of ASCII plain text, the naming conventions for the .txt file,
and an incorporation by reference statement to be included in the
specification, as per Sec. 1.77(b)(5).
Section 1.58(e) is proposed to be added to state that ``Large
Tables'' submitted via the USPTO patent electronic filing system must
not exceed 25 MB, and file compression is not permitted. It is noted
that when submitting via the USPTO patent electronic filing system, it
is possible to submit multiple files that are 25 MB or less in size, as
per the Legal Framework for Patent Electronic System cited supra.
Section 1.58(f) is proposed to be added to specify the technical
requirements for ``Large Tables'' submitted on read-only optical discs
in compliance with Sec. 1.52(e) and that compression is permitted.
Section 1.58(f) also specifies the permitted manner of file
compression.
Section 1.58(g) is proposed to be added to provide the procedure
that would be applicable should an amendment of one or more ``Large
Tables'' be required. If an amendment is required to be made to a
``Large Table,'' then a replacement submission via the USPTO patent
electronic filing system or on duplicate read-only optical discs would
be necessary. An updated incorporation by reference statement would be
required along with the necessary statement regarding any deletions,
replacements or addition to the ASCII plain text file and a statement
that the replacement ASCII plain text file contains no new matter.
Section 1.58(h) is proposed to be added to specify that should
``Large Tables'' be submitted as an ASCII plain text file on the
application filing date,
[[Page 28306]]
but no incorporation by reference of the material contained therein has
been made, an amendment containing a separate paragraph incorporating
by reference the material contained in the ASCII plain text file, as
per Sec. 1.77(b)(5), will be required.
Section 1.58(i) is proposed to be added to require that any read-
only optical disc for a ``Large Table'' be submitted in duplicate.
Section 1.58(i) sets forth the criteria for labeling and necessary
statements as to the identity of the read-only optical discs. This
section indicates how the USPTO will treat the submission of the two
read-only optical discs that are not identical to each other. Duplicate
copies for ``Large Tables'' are required to be submitted since the OPAP
keeps a first copy for record retention purposes and a second copy in
an artifact folder for use by the examiner during the patent
examination process.
Section 1.58(j) is proposed to be added to require that any
amendment to the information on a read-only optical disc must be by way
of a replacement read-only optical disc, in compliance with Sec.
1.58(g), where the replacement read-only optical disc and copy must be
labeled ``COPY 1 REPLACEMENT MM/DD/YYYY'' (with the month, day, and
year of creation indicated) and ``COPY 2 REPLACEMENT MM/DD/YYYY,''
respectively. This section indicates how the USPTO will treat the
submission of the two replacement read-only optical discs that are not
identical to each other.
Section 1.71: Section 1.71(f) is proposed to be revised to clarify
that a ``Sequence Listing,'' if required or submitted under Sec.
1.821(c), should be submitted on a separate sheet. This is directed to
those submissions of the ``Sequence Listing'' submitted on physical
sheets of paper or submitted as a PDF image file via the USPTO patent
electronic filing system. In such cases where there is a separate
``Sequence Listing'' and a separate CRF of the ``Sequence Listing,''
the ``Sequence Listing'' must be on a separate sheet(s).
Section 1.77: Section 1.77(b)(5) is proposed to be revised to
clarify when an incorporation by reference is needed. The proposed rule
change provides for incorporation by reference of ASCII plain text
files submitted via the USPTO patent electronic filing system or on one
or more read-only optical discs for a ``Computer Program Listing
Appendix,'' a ``Sequence Listing,'' or ``Large Tables,'' as provided
for in Sec. Sec. 1.96(c), 1.821(c), or 1.58(c), respectively. The
proposed incorporation by reference statement would identify the names
of each ASCII plain text file and specify, if applicable, the files
contained on each of the read-only optical discs, their dates of
creation, and the sizes of each ASCII plain text file in bytes.
Section 1.77(b)(13) is proposed to be revised to clarify that the
``Sequence Listing'' required by Sec. 1.821(c), submitted on physical
sheets of paper or as a PDF image file of the ``Sequence Listing,''
should follow the other sections of the specification.
Section 1.96: Section 1.96(a) is proposed to be revised to replace
``printout'' with ``document.''
Section 1.96(c) is proposed to be revised to set forth the
requirements that apply to any ``Computer Program Listing Appendix''
that will not be part of the printed patent specification. The appendix
must be submitted as an electronic document in ASCII plain text,
whether submitted via the USPTO patent electronic filing system or on a
read-only optical disc, in compliance with Sec. 1.52(e). Proposed
requirements for the ``Computer Program Listing Appendix'' include that
it must be incorporated by reference in the specification, as set forth
in Sec. 1.77(b)(5), and have certain computer compatibilities (Sec.
1.96(c)(1)), naming convention adherences (Sec. 1.96(c)(2)), and size
limitations (Sec. 1.96(c)(3)).
Section 1.96(c)(4) is proposed to be added to state requirements
(i) through (vi) where the ``Computer Program Listing Appendix'' is
submitted on a read-only optical disc, in compliance with Sec.
1.52(e).
Section 1.96(c)(5) is proposed to be added to state requirements
(i) through (iv) for amendments to delete, replace, or add to the
information of a ``Computer Program Listing Appendix'' submitted in
electronic form in ASCII plain text.
Section 1.96(c)(6) is proposed to be added to indicate that should
a ``Computer Program Listing Appendix'' be present on the filing date
of the application without an express incorporation by reference in the
specification relating to the material contained in the ASCII plain
text file, in accordance with Sec. 1.77(b)(5), then an amendment to
include such a paragraph in the specification will be required.
Section 1.96(c)(7) is proposed to be added to indicate that a
submission of a ``Computer Program Listing Appendix'' on a read-only
optical disc must be completed in duplicate, since the processing by
the USPTO of a ``Computer Program Listing Appendix'' submitted on a
read-only optical disc involves keeping a first copy for record
retention purposes and using a second copy during the examination
process. The new section sets forth the criteria for labeling and
necessary statements as to the identity of the read-only optical discs.
This proposed section indicates how the USPTO will treat the submission
of the two read-only optical discs should they not be identical.
Section 1.121: Section 1.121(b) is proposed to be revised, and
Sec. 1.121(b)(6) is proposed to be added, to clarify that ``Large
Tables'' in accordance with Sec. 1.58(c), a ``Computer Program Listing
Appendix'' in accordance with Sec. 1.96(c)(5) and (7), and a
``Sequence Listing'' or CRF in accordance with Sec. 1.825 must be
amended in accordance with Sec. 1.58(g), Sec. 1.96(c)(5), and Sec.
1.825, respectively.
Section 1.173: The heading of Sec. 1.173(b)(1) is proposed to be
revised to reflect that, in a reissue application, changes to the
claims, ``Large Tables'' (Sec. 1.58(c)), a ``Computer Program Listing
Appendix'' (Sec. 1.96(c)), or a ``Sequence Listing'' (Sec. 1.821(c))
are made in a different manner from changes to other parts of the
specification.
The manner of making changes to the specification, other than to
the claims, set forth in current Sec. 1.173(b)(1) is proposed to be
moved to new Sec. 1.173(b)(1)(i). New Sec. 1.173(b)(1)(i) specifies
that it does not apply to changes to ``Large Tables'' (Sec. 1.58(c)),
a ``Computer Program Listing Appendix'' (Sec. 1.96(c)), or a
``Sequence Listing'' (Sec. 1.821(c)), in addition to not applying to
changes to the claims. Additionally, the language from current Sec.
1.173(b)(1) stating that the paragraph is not applicable to discs is
proposed to not be included in new Sec. 1.173(b)(1)(i).
Section Sec. 1.173(b)(1)(ii) is proposed to be added to specify
that changes to ``Large Tables,'' a ``Computer Program Listing
Appendix,'' or a ``Sequence Listing'' must be made in accordance with
Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5) for a ``Computer
Program Listing Appendix,'' and Sec. 1.825 for a ``Sequence Listing.''
Section 1.173(d) is proposed to be revised to exclude changes to
``Large Tables,'' a ``Computer Program Listing Appendix,'' or a
``Sequence Listing'' from the changes that must be shown by markings in
a reissue application.
Section Sec. 1.173(d)(2) is proposed to be revised to delete the
following: ``except for amendments submitted on compact discs
(Sec. Sec. 1.96 and 1.821(c)). Matter added by reissue on compact
discs must be preceded with `' and end with `' to properly
identify the material being added.''
Section 1.530: The heading of Sec. 1.530(d)(1) is proposed to be
revised to reflect that, in a reexamination proceeding, changes to the
claims, ``Large Tables'' (Sec. 1.58(c)), a ``Computer Program Listing
Appendix'' (Sec. 1.96(c)),
[[Page 28307]]
and a ``Sequence Listing'' (Sec. 1.821(c)) are made in a different
manner from changes to the other parts of the specification.
The manner of making changes to the specification, other than to
the claims, set forth in current Sec. 1.530(d)(1) is proposed to be
moved to new Sec. 1.530(d)(1)(i). New Sec. 1.530(d)(1)(i) specifies
that it does not apply to changes to ``Large Tables'' (Sec. 1.58(c)),
a ``Computer Program Listing Appendix'' (Sec. 1.96(c)), and a
``Sequence Listing'' (Sec. 1.821(c)), in addition to not applying to
changes to the claims.
Section 1.530(d)(1)(ii) is proposed to be added to specify that
changes to ``Large Tables,'' a ``Computer Program Listing Appendix,''
or a ``Sequence Listing'' must be made in accordance with Sec. 1.58(g)
for ``Large Tables,'' Sec. 1.96(c)(5) for a ``Computer Program Listing
Appendix,'' and Sec. 1.825 for a ``Sequence Listing.''
Section 1.821: Section 1.821(a) is proposed to be revised to remove
all prior references to WIPO Standard ST.25 (1998) and instead cross-
reference new Appendices A through F to part 1 of 37 CFR, subpart G,
which would contain the updated 2009 version of the tables from WIPO
Standard ST.25.
Section 1.821(c) is proposed to be revised to delete references to
a paper or compact disc copy (Sec. 1.52(e)), delete discussion of
sequence identifiers, and indicate that the criteria for submission of
a ``Sequence Listing,'' except for national stage entry under Sec.
1.495(b)(1), is set forth in newly proposed Sec. 1.821(c)(1)-(3).
Information about sequence identifiers has been moved to Sec.
1.823(a).
Section 1.821(c)(1) is proposed to be added to require that the
``Sequence Listing'' can be submitted as an ASCII plain text file via
the USPTO patent electronic filing system or on a read-only optical
disc copy, where the form and format of the ``Sequence Listing''
conforms to Sec. 1.824 and an incorporation by reference statement as
required by Sec. 1.52(e) is provided. Section 1.821(c)(2) is proposed
to be added to permit submission of a ``Sequence Listing'' as a PDF
file via the USPTO patent electronic filing system. Section 1.821(c)(3)
is proposed to be added to permit the submission of a ``Sequence
Listing'' on physical sheets of paper.
Section 1.821(d) is proposed to be revised to add that where a
sequence is presented in a drawing, reference must be made to the
sequence by use of a sequence identifier, either in the drawing or in
the Brief Description of the Drawings, where the correlation between
multiple sequences in the drawing and their sequence identifiers in the
Brief Description is clear. A sequence found in a drawing sheet is not
a ``Sequence Listing'' under Sec. 1.821(c) or (e). Therefore, a
separate ``Sequence Listing'' would be required to comply with Sec.
1.821(c). If the ``Sequence Listing'' was submitted as a PDF image file
via the USPTO patent electronic filing system or on physical sheets of
paper, a separate CRF of the ``Sequence Listing'' would be required to
comply with Sec. 1.821(e).
Section 1.821(e)(1) is proposed to be added to set forth the
requirements in Sec. 1.821(e)(1)(i) for submission of a CRF of the
``Sequence Listing,'' in compliance with Sec. 1.824, when a ``Sequence
Listing'' was submitted as a PDF image file via the USPTO patent
electronic filing system or on physical sheets of paper for an
application filed under 35 U.S.C. 111(a). The proposed rule (Sec.
1.821(e)(1)(ii)) also indicates that a statement is required to confirm
that the CRF is identical to the ``Sequence Listing'' under Sec.
1.821(c), when the submission of the ``Sequence Listing'' under Sec.
1.821(c) was on physical sheets of paper or as a PDF image file via the
USPTO patent electronic filing system.
Section 1.821(e)(2) is proposed to be added to set forth the
requirements where the ``Sequence Listing'' under Sec. 1.821(c) in an
application submitted under 35 U.S.C. 371 is in a PDF file (Sec.
1.821(c)(2)) or on physical sheets of paper (Sec. 1.821(c)(3)), and
not also as an ASCII plain text file, in compliance with Sec. 1.824
(Sec. 1.821(c)(1)). In such situations, the following are required:
(1) A copy of the ``Sequence Listing'' in CRF, in accordance with the
requirements of Sec. 1.824 (Sec. 1.821(e)(2)(i)); and (2) a statement
that the sequence information contained in the CRF, submitted under
Sec. 1.821(e)(2)(i), is identical to the sequence information
contained in the ``Sequence Listing'' submitted as a PDF image file
(1.821(c)(2)) or on physical sheets of paper (1.821(c)(3)).
Section 1.821(e)(3) is proposed to be added to set forth the
requirements where a ``Sequence Listing'' in ASCII plain text format,
in compliance with Sec. 1.824, has not been submitted for an
international application under the Patent Cooperation Treaty (PCT);
this application contains disclosures of nucleotide and/or amino acid
sequences, as defined in paragraph (a) of this section and is to be
searched by the United States International Searching Authority or
examined by the United States International Preliminary Examining
Authority. In such situations, the following are required: (1) A copy
of the ``Sequence Listing'' in CRF, in accordance with the requirements
of Sec. 1.824 (Sec. 1.821(e)(3)(i)); (2) a late furnishing fee for
providing a ``Sequence Listing'' in response to an invitation, as set
forth in Sec. 1.445(a)(5) (Sec. 1.821(e)(3)(ii)); and (3) a statement
that the sequence information contained in the CRF submitted under
Sec. 1.821(e)(3)(i) does not go beyond the disclosure in the
international application as filed, or a statement that the information
recorded in the ASCII plain text file submitted under Sec.
1.821(e)(3)(i) is identical to the sequence listing contained in the
international application as filed, as applicable (Sec.
1.821(e)(3)(iii)).
Section 1.821(e)(4) is proposed to be added to state that the CRF
may not be retained as a part of the patent application file.
Section 1.821(f) is proposed to be reserved. The text previously
found in this section is now in Sec. 1.821(e)(2)(iii).
Section 1.821(g) is proposed to be revised to delete reference to
Sec. 1.821(f). Additionally, Sec. 1.821(g) is proposed to be revised
to state that any amendment to add or replace a ``Sequence Listing''
and CRF copy thereof must be submitted in accordance with the
requirements of Sec. 1.825.
Section 1.821(h) is proposed to be revised to reference paragraphs
(e)(3) of this section instead of paragraphs (b) through (f). Section
1.821(h) is also proposed to be revised to add that a late furnishing
fee, as set forth in Sec. 1.445(a)(5), is required where a ``Sequence
Listing'' under PCT Rule 13ter is provided.
Section 1.822: Section 1.822(b) is proposed to be revised to remove
all prior references to WIPO Standard ST.25 (1998) and instead cross-
reference new Appendices A through F to part 1 of 37 CFR, subpart G,
which would contain the updated 2009 version of the standard.
Therefore, the statement regarding permission for incorporation by
reference and information about the availability of ST.25 from WIPO's
website is deleted.
Section 1.822(c)(1) is proposed to be revised to remove the prior
reference to WIPO Standard ST.25 (1998) and instead cross-reference new
Appendix A to part 1 of 37 CFR, subpart G, which would contain the
updated 2009 version of the standard.
Section 1.822(c)(3) is proposed to be rewritten to replace
instances of ``typed'' with ``listed.''
Section 1.822(c)(5) is proposed to be rewritten to replace
``presented'' with ``represented.''
Section 1.822(c)(6) is proposed to be rewritten to delete ``be
marked'' and instead state ``appear.''
[[Page 28308]]
Section 1.822(d)(1) is proposed to be revised to remove the prior
reference to WIPO Standard ST.25 (1998) and instead cross-reference new
Appendix C to part 1 of 37 CFR, subpart G, which would contain the
updated 2009 version of the standard. When providing reference to the
sequence in the text of the description or claims, the numeric sequence
identifier is preceded by SEQ ID NO: Or the like, even if the actual
sequence is also embedded in the text of the description or claims of
the patent application. The use of SEQ ID NO: Is preferred but
including ``or the like'' is intended to ensure that a formalities
notice is not sent when an application uses, for example, ``SEQ NO.''
or ``Seq. Id. No.'' or any similar identification for an amino acid or
nucleotide sequence in the specification or claims where it is clear
that a sequence from the ``Sequence Listing'' is shown in the
description or claims.
Section 1.822(d)(3) is proposed to be rewritten to replace
``presented'' with ``represented.''
Section 1.822(d)(4) is proposed to be rewritten to replace
``presented'' with ``represented.''
Section 1.822(d)(5) is proposed to be rewritten to replace the
second occurrence of ``presented'' with ``represented.''
Section 1.822(e) is proposed to be rewritten to replace ``that is
made up'' with the term ``composed.''
Section 1.823: The title of Sec. 1.823 is proposed to be rewritten
as ``Requirements for content of a `Sequence Listing' part of the
specification.''
Section 1.823(a) is proposed to be rewritten to enumerate in Sec.
1.823(a)(1) through (8) the content requirements for a ``Sequence
Listing'' previously contained in Sec. Sec. 1.821(c), 1.823(a)(1),
1.823(a)(2), and 1.823(b). Such requirements include, but are not
limited to, sequence identifiers, the order and presentation of items
of information, mandatory and optional information, the format as to
line spacing, and the use of numeric identifiers.
Section 1.823(b)(1) is proposed to include a requirement for
applications other than an international application in the
international stage to contain an express incorporation by reference of
the material submitted as an ASCII plain text file via the USPTO patent
electronic filing system or on read-only optical disc(s) into the
specification of the patent application to identify the name of the
file, the date of creation, and the size of the file in bytes.
Section 1.823(b)(2) is proposed to specifically exempt the
incorporation by reference requirement in Sec. 1.823(b)(1) from
international applications during the international stage.
Section 1.823(b)(3) is proposed to be added to specifically set
forth the format and content for a ``Sequence Listing'' that is
submitted either as a PDF image file via the USPTO patent electronic
filing system or on physical sheets of paper, as enumerated in Sec.
1.823(b)(3)(i) through (vi).
Section 1.824: The title of Sec. 1.824 is proposed to be rewritten
as ``Form and format for a nucleotide and/or amino acid sequence
submission as an ASCII plain text file.''
Section 1.824(a) is proposed to be reorganized for clarity and to
apply to any ``Sequence Listing'' submission as an ASCII plain text
file, rather than only to the CRF of a ``Sequence Listing.'' Section
1.824(a)(1) is proposed to set forth the computer compatibilities and
operating systems permitted. Section 1.824(a)(2) is proposed to
indicate that ASCII plain text is required to be used, that all
printable characters are permitted, and that no nonprintable characters
are permitted, except ASCII Carriage Return plus ASCII Line Feed (CRLF)
or Line Feed (LF) as line terminators. Section 1.824(a)(3) is proposed
to set forth the naming convention for the ASCII plain text file of the
``Sequence Listing.'' Section 1.824(a)(4) is proposed to indicate that
no more than 74 printable characters can be present on any given line.
This number represents a change from current rules (where 72 characters
are permitted). This change is intended to conform to the number of
characters of a sequence listing as printed in a granted patent or a
pre-grant publication.
Section 1.824(a)(5) is proposed to indicate that pagination is not
permitted and that the ASCII plain text file must be one continuous
file with no hard page breaks and no page numbering.
Section 1.824(b) is proposed to indicate that the ASCII plain text
file must contain a copy of a single ``Sequence Listing'' in a single
file and may be submitted through either the USPTO patent electronic
filing system or on read-only optical disc(s), in compliance with Sec.
1.52(e). Section 1.824(b)(2) is proposed to provide that file
compression may be used and to define the parameters for file
compression for submission on a read-only optical disc. Section 1.824
is proposed to be further revised to eliminate obsolete media on which
the CRF of a ``Sequence Listing'' may be submitted. Section 1.824(c) is
proposed to be eliminated, since the types of media available are
specifically enumerated in Sec. 1.52(e). Section 1.824(d) is proposed
to be eliminated, since the same provision is now included in Sec.
1.52(e)(6).
Section 1.825: Sections 1.825(a) and (b) are proposed to be
rewritten to distinguish between a newly added ``Sequence Listing'' and
an amended/replacement ``Sequence Listing'' submission, respectively.
Sections 1.825(a) and (b) are proposed to be rewritten to state when a
new or amended/replacement copy of the CRF is also required upon
submission of a ``Sequence Listing.''
Section 1.825(a) is proposed to be amended to provide for
submission of a ``Sequence Listing'' not present on the application
filing date (1) as an ASCII plain text file via either the USPTO patent
electronic filing system or on a read-only optical disc, (2) as a PDF
image file via the USPTO patent electronic filing system, or (3) on
physical sheets of paper. The amendment adding the ``Sequence Listing''
must include a request that the amendment be made in one of two ways.
First, a ``Sequence Listing'' submitted as an ASCII plain text file (in
accordance with Sec. 1.825(a)(2)(i)) must be incorporated by reference
in a separate paragraph of the specification. Second, a ``Sequence
Listing'' submitted as a PDF image file via the USPTO patent electronic
filing system (in accordance with Sec. 1.825(a)(2)(ii)) or on physical
sheets of paper (in accordance with Sec. 1.825(a)(2)(iii)) must be
placed after the abstract of the disclosure. Additionally, the
``Sequence Listing'' must be submitted together with two statements.
The first statement must indicate the basis for the amendment, with
specific references to particular parts of the application as
originally filed (specification, claims, drawings) for all sequence
data in the ``Sequence Listing'' (Sec. 1.821(a)(3)). The second
statement must indicate that the ``Sequence Listing'' contains no new
matter (Sec. 1.821(a)(4)). Finally, if needed, Sec. 1.825(a)(5)
provides that a new or substitute CRF must be submitted together with a
statement, pursuant to Sec. 1.825(a)(6), that the sequence information
contained in the CRF is the same as the sequence information contained
in the ``Sequence Listing'' that had been submitted as a PDF image file
via the USPTO patent electronic filing system or on physical sheets of
paper.
Section 1.825(b) is proposed to be updated to require an amended/
replacement ``Sequence Listing'' submitted: (1) As an ASCII plain text
file via either the USPTO patent electronic filing system or on a read-
[[Page 28309]]
only optical disc (Sec. 1.825(b)(1)(i)), (2) as a PDF image file via
the USPTO patent electronic filing system (Sec. 1.825(b)(1)(ii)), or
(3) on physical sheets of paper (Sec. 1.825(b)(1)(iii)). The amended/
replacement ``Sequence Listing'' must include a request that it be made
in one of two ways. First, a request that the amended/replacement
``Sequence Listing,'' submitted as an ASCII plain text file, is
incorporated by reference in a separate paragraph of the specification
(replacing any prior such paragraph, as applicable) (Sec.
1.825(b)(2)). The second way for such a request is by placing, after
the abstract of the disclosure, the amended/replacement ``Sequence
Listing'' that was submitted as a PDF image file via the USPTO patent
electronic filing system or on physical sheets of paper (replacing any
prior ``Sequence Listing,'' as applicable).
The amended/replacement ``Sequence Listing'' must be submitted
together with three statements. The first statement must identify the
location of all deletions, replacements, or additions to the ``Sequence
Listing'' (Sec. 1.825(b)(3)). The second statement must indicate the
basis for the amendment, with specific references to particular parts
of the application as originally filed (specification, claims,
drawings) for all amended sequence data in the replacement ``Sequence
Listing'' (Sec. 1.825(b)(4)). The third statement must indicate that
the replacement ``Sequence Listing'' contains no new matter (Sec.
1.825(b)(5)). Finally, if needed, a new or substitute CRF with the
amendment incorporated therein (Sec. 1.825(b)(6)) must be submitted
together with a statement that the sequence information contained in
the CRF is the same as the sequence information contained in the
replacement ``Sequence Listing'' submitted as a PDF image file via the
USPTO patent electronic filing system or on physical sheets of paper
(Sec. 1.825(b)(7)).
Section 1.825(c) is proposed to replace current Sec. 1.825(c),
which is proposed to be moved to Sec. 1.825(d). Section 1.825(c)
relates to the required incorporation by reference statement when
submitting a ``Sequence Listing'' under Sec. 1.821(c)(1). Should the
application as originally filed not contain the incorporation by
reference, then the application must be amended to contain such an
incorporation by reference.
Section 1.825(d) is proposed to contain the material from current
Sec. 1.825(c).
Subpart G of part 1: Appendices A through F are proposed to be
added, explicitly incorporating the text of Tables 1-6, Appendix 2,
WIPO Standard ST.25 (2009) into the CFR. Appendix G is proposed to be
added to incorporate the table that was previously located in Sec.
1.823.
Rulemaking Considerations
A. Administrative Procedure Act: The changes proposed in this
rulemaking involve rules of agency practice and procedure, and/or
interpretive rules. See Bachow Commc'ns Inc. v. FCC, 237 F.3d 683, 690
(D.C. Cir. 2001) (rules governing an application process are procedural
under the Administrative Procedure Act); Inova Alexandria Hosp. v.
Shalala, 244 F.3d 342, 350 (4th Cir. 2001) (rules for handling appeals
are procedural where they do not change the substantive standard for
reviewing claims); Nat'l Org. of Veterans' Advocates v. Sec'y of
Veterans Affairs, 260 F.3d 1365, 1375 (Fed. Cir. 2001) (rule that
clarifies interpretation of a statute is interpretive).
Accordingly, prior notice and opportunity for public comment for
the changes proposed in this rulemaking are not required pursuant to 5
U.S.C. 553(b) or (c), or any other law. See Cooper Techs. Co. v. Dudas,
536 F.3d 1330, 1336-37 (Fed. Cir. 2008) (stating that 5 U.S.C. 553, and
thus 35 U.S.C. 2(b)(2)(B), do not require notice and comment rulemaking
for ``interpretative rules, general statements of policy, or rules of
agency organization, procedure, or practice'' (quoting 5 U.S.C.
553(b)(A))). However, the USPTO has chosen to seek public comment
before implementing the rule to benefit from the public's input.
B. Regulatory Flexibility Act: Under the Regulatory Flexibility Act
(5 U.S.C. 601 et seq.), whenever an agency is required by 5 U.S.C. 553
(or any other law) to publish a notice of proposed rulemaking (NPRM),
the agency must prepare and make available for public comment an
Initial Regulatory Flexibility Analysis, unless the agency certifies
under 5 U.S.C. 605(b) that the proposed rule, if implemented, will not
have a significant economic impact on a substantial number of small
entities. 5 U.S.C. 603, 605.
For the reasons set forth herein, the Senior Counsel for Regulatory
and Legislative Affairs of the USPTO has certified to the Chief Counsel
for Advocacy of the Small Business Administration that this rule will
not have a significant economic impact on a substantial number of small
entities. See 5 U.S.C. 605(b).
The USPTO proposes to amend the rules of practice to permit higher-
capacity physical media to be submitted to accommodate patent
applications for certain inventions that require significant data in
ASCII text format that exceed the capacity of the Office's electronic
filing system. Additionally, extraction of compressed data files, which
had not been permitted in the past for certain submissions, would be
permitted if compliant with certain proposed new procedures. Other
rules relating to certain obsolete and non-secure methods of presenting
data would be eliminated. Lastly, this NPRM would remove an applicant's
ability to rely on a previously submitted CRF of required sequence
information (i.e., CRF transfer requests are eliminated). In light of
the availability to download a ``Sequence Listing'' from granted U.S.
patents and U.S. patent application publications via Public PAIR in the
Supplemental Content tab, there is no longer a need for a CRF transfer.
This rulemaking would make more flexible the process for submitting
large amounts of data and streamline other procedural steps related to
data files associated with patent applications. This rulemaking's
proposed changes are largely procedural in nature, and do not impose
any additional requirements or fees on applicants. For the foregoing
reasons, the changes proposed in this NPRM will not have a significant
economic impact on a substantial number of small entities.
C. Executive Order 12866 (Regulatory Planning and Review): This
rulemaking has been determined to be not significant for purposes of
Executive Order 12866 (Sept. 30, 1993).
D. Executive Order 13563 (Improving Regulation and Regulatory
Review): The USPTO has complied with Executive Order 13563 (Jan. 18,
2011). Specifically, to the extent feasible and applicable, the USPTO
has: (1) Reasonably determined that the benefits of the rule justify
its costs; (2) tailored the rule to impose the least burden on society
consistent with obtaining the agency's regulatory objectives; (3)
selected a regulatory approach that maximizes net benefits; (4)
specified performance objectives; (5) identified and assessed available
alternatives; (6) involved the public in an open exchange of
information and perspectives among experts in relevant disciplines,
affected stakeholders in the private sector, and the public as a whole,
and provided online access to the rulemaking docket; (7) attempted to
promote coordination, simplification, and harmonization across
government agencies and identified goals designed to promote
innovation; (8) considered approaches that reduce burdens while
maintaining flexibility and freedom of choice for the public; and (9)
ensured
[[Page 28310]]
the objectivity of scientific and technological information and
processes.
E. Executive Order 13132 (Federalism): This rulemaking does not
contain policies with federalism implications sufficient to warrant
preparation of a Federalism Assessment under Executive Order 13132
(Aug. 4, 1999).
F. Executive Order 13175 (Tribal Consultation): This rulemaking
will not (1) have substantial direct effects on one or more Indian
tribes; (2) impose substantial direct compliance costs on Indian tribal
governments; or (3) preempt tribal law. Therefore, a tribal summary
impact statement is not required under Executive Order 13175 (Nov. 6,
2000).
G. Executive Order 13211 (Energy Effects): This rulemaking is not a
significant energy action under Executive Order 13211 because this
rulemaking is not likely to have a significant adverse effect on the
supply, distribution, or use of energy. Therefore, a Statement of
Energy Effects is not required under Executive Order 13211 (May 18,
2001).
H. Executive Order 12988 (Civil Justice Reform): This rulemaking
meets applicable standards to minimize litigation, eliminate ambiguity,
and reduce burden as set forth in sections 3(a) and 3(b)(2) of
Executive Order 12988 (Feb. 5, 1996).
I. Executive Order 13045 (Protection of Children): This rulemaking
does not concern an environmental risk to health or safety that may
disproportionately affect children under Executive Order 13045 (Apr.
21, 1997).
J. Executive Order 12630 (Taking of Private Property): This
rulemaking will not effect a taking of private property or otherwise
have taking implications under Executive Order 12630 (Mar. 15, 1988).
K. Congressional Review Act: Under the Congressional Review Act
provisions of the Small Business Regulatory Enforcement Fairness Act of
1996 (5 U.S.C. 801 et seq.), prior to issuing any final rule, the USPTO
will submit a report containing the final rule and other required
information to the United States Senate, the United States House of
Representatives, and the Comptroller General of the Government
Accountability Office. The changes in this rulemaking are not expected
to result in an annual effect on the economy of $100 million or more, a
major increase in costs or prices, or significant adverse effects on
competition, employment, investment, productivity, innovation, or the
ability of United States-based enterprises to compete with foreign-
based enterprises in domestic and export markets. Therefore, this
rulemaking is not expected to result in a ``major rule'' as defined in
5 U.S.C. 804(2).
L. Unfunded Mandates Reform Act of 1995: The changes set forth in
this rulemaking do not involve a Federal intergovernmental mandate that
will result in the expenditure by State, local, and tribal governments,
in the aggregate, of $100 million (as adjusted) or more in any one
year, or a Federal private sector mandate that will result in the
expenditure by the private sector of $100 million (as adjusted) or more
in any one year, and will not significantly or uniquely affect small
governments. Therefore, no actions are necessary under the provisions
of the Unfunded Mandates Reform Act of 1995. See 2 U.S.C. 1501 et seq.
M. National Environmental Policy Act of 1969: This rulemaking will
not have any effect on the quality of the environment and is thus
categorically excluded from review under the National Environmental
Policy Act of 1969. See 42 U.S.C. 4321 et seq.
N. National Technology Transfer and Advancement Act of 1995: The
requirements of section 12(d) of the National Technology Transfer and
Advancement Act of 1995 (15 U.S.C. 272 note) are not applicable because
this rulemaking does not contain provisions that involve the use of
technical standards.
O. Paperwork Reduction Act of 1995: The Paperwork Reduction Act of
1995 (44 U.S.C. 3501-3549) requires that the USPTO consider the impact
of paperwork and other information collection burdens imposed on the
public. In accordance with section 3507(d) of the Paperwork Reduction
Act of 1995, the majority of the paperwork and other information
collection burdens discussed in this proposed rule have already been
approved under the following Office of Management and Budget (OMB)
Control Numbers: 0651-0024 (Sequence Listing), 0651-0031 (Patent
Processing), 0651-0032 (Initial Patent Applications), and 0651-0064
(Patent Reexaminations and Supplemental Examinations).
Modifications to 0651-0024 because of this proposed rulemaking will
be submitted to OMB for approval prior to this rule becoming effective.
Modifications include the removal of the Request for Transfer of a
Computer Readable Form Under 37 CFR 1.821(e) (PTO/SB/93), which will
result in a slight reduction in burden associated with this information
collection. The USPTO estimates that this information collection's
annual burden will decrease by 1,550 responses and 155 burden hours.
These burden estimates are based on the current OMB approved burdens
(response volumes) associated with this information collection, which
may be different from any forecasts mentioned in other parts of this
proposed rule.
The changes discussed in this proposed rule do not affect the
information collection requirements or burdens associated with 0651-
0031, 0651-0032 and 0651-0064 listed above; therefore, the USPTO does
not plan to take any additional actions on these information
collections as a result of this rulemaking. Notwithstanding any other
provision of law, no person is required to respond to, nor shall a
person be subject to a penalty for failure to comply with, a collection
of information subject to the requirements of the Paperwork Reduction
Act unless that collection of information has a currently valid OMB
control number.
P. E-Government Act Compliance: The USPTO is committed to
compliance with the E-Government Act to promote the use of the internet
and other information technologies, to provide increased opportunities
for citizen access to Government information and services, and for
other purposes.
List of Subjects in 37 CFR Part 1
Administrative practice and procedure, Biologics, Courts, Freedom
of information, Inventions and patents, Reporting and recordkeeping
requirements, Small businesses.
For the reasons stated in the preamble and under the authority
contained in 35 U.S.C. 2, as amended, the USPTO proposes to amend 37
CFR part 1 as follows:
PART 1--RULES OF PRACTICE IN PATENT CASES
0
1. The authority citation for 37 CFR part 1 continues to read as
follows:
Authority: 35 U.S.C. 2(b)(2), unless otherwise noted.
0
2. Amend Sec. 1.52 by revising the heading and paragraphs (e) and (f)
to read as follows:
Sec. 1.52 Language, paper, writing, margins, read-only optical disc
specifications.
* * * * *
(e) Electronic documents submitted on a read-only optical disc that
are to become part of the permanent United States Patent and Trademark
Office records in the file of a patent application, reexamination, or
supplemental examination proceeding. (1) The following documents may be
submitted to the Office on a read-only
[[Page 28311]]
optical disc in compliance with this paragraph:
(i) A ``Computer Program Listing Appendix'' (see Sec. 1.96(c));
(ii) A ``Sequence Listing'' (submitted under Sec. 1.821(c) in
compliance with Sec. 1.824); or
(iii) ``Large Tables'' (see Sec. 1.58(c)).
(2) Read-only optical disc as used in this part means a finalized
disc in conformance with International Organization for Standardization
(ISO) 9660, on which the data is recorded so it is permanent and cannot
be changed or erased, and is one of:
(i) Compact Disc-Read-Only Memory (CD-ROM) or a Compact Disc-
Recordable (CD-R); or
(ii) Digital Video Disc-Recordable (DVD-R or DVD+R);
(3) Each read-only optical disc must conform to the following
requirements:
(i) Computer compatibility: PC or Mac[supreg];
(ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], MacOS[supreg], or Unix[supreg]/Linux[supreg];
(iii) The contents of each read-only optical disc must be in
American Standard Code for Information Interchange (ASCII) plain text
and if compressed, must be compressed in accordance with Sec. Sec.
1.58, 1.96, and 1.824, as applicable.
(4) Each read-only optical disc must be enclosed in a hard case
within an unsealed, padded, and protective mailing envelope, and must
be accompanied by a transmittal letter in accordance with paragraph (a)
of this section, including the following information:
(i) First-named inventor (if known);
(ii) Title of the invention;
(iii) Attorney docket or file reference number (if applicable);
(iv) Application number and filing date (if known);
(v) The operating system (MS-DOS[supreg], MS-Windows[supreg], Mac
OS[supreg], or Unix[supreg]/Linux[supreg]) used to produce the disc;
and
(vi) The file(s) contained on the read-only optical disc, including
the name of the file, the size of the file in bytes, and the date of
creation.
(5) Each read-only optical disc must have a label permanently
affixed thereto on which the following information has been hand-
printed or typed:
(i) First-named inventor (if known);
(ii) Title of the invention;
(iii) Attorney docket or file reference number (if applicable);
(iv) Application number and filing date (if known);
(v) Date on which the data were recorded on the read-only optical
disc; and
(vi) Disc order (e.g., ``1 of X''), if multiple read-only optical
discs are submitted.
(6) Read-only optical discs will not be returned to the applicant
and may not be retained as part of the patent application file.
(7) Any amendment to the information on a read-only optical disc
must be by way of a replacement read-only optical disc, in compliance
with Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5) for a
``Computer Program Listing Appendix,'' and Sec. 1.825(b) for a
``Sequence Listing'' or Computer Readable Form (CRF) of a ``Sequence
Listing.''
(8) The specification must contain an incorporation by reference of
the material on each read-only optical disc in a separate paragraph
(Sec. 1.77(b)(5)), identifying the name of each file, their date of
creation, and their size in bytes, except for an international
application in the international stage. The Office may require the
applicant to amend the specification to include the material
incorporated by reference.
(9) If a file is unreadable, it will be treated as not having been
submitted, and a notice will be issued to supply a compliant
submission.
(f) Determining application size fees for applications containing
electronic documents submitted on a read-only optical disc or via the
USPTO patent electronic filing system--(1) Submission on Read-Only
Optical Discs: The application size fee required by Sec. 1.16(s) or
1.492(j), for an application component submitted in part on a read-only
optical disc in compliance with paragraph (e) of this section, shall be
determined such that each three kilobytes of content submitted on a
read-only optical disc shall be counted as a sheet of paper. Excluded
from this determination is any ASCII plain text file submitted on a
read-only optical disc under paragraph (e) of this section containing:
(i) Any ``Sequence Listing'' or CRF of a ``Sequence Listing'' in
compliance with Sec. 1.821(c) or (e); or
(ii) Any ``Computer Program Listing Appendix'' in compliance with
Sec. 1.96(c).
(2) Submission via the USPTO Patent Electronic Filing System: The
application size fee required by Sec. 1.16(s) or 1.492(j), for an
application submitted in whole or in part via the USPTO patent
electronic filing system, shall be determined such that the paper size
equivalent will be considered to be 75% of the number of sheets of
paper present in the specification and drawings of the application when
entered into the Office file wrapper after being rendered by the USPTO
patent electronic filing system. Excluded from this determination is
any ASCII plain text file submitted via the USPTO patent electronic
filing system containing:
(i) Any ``Sequence Listing'' or CRF of a ``Sequence Listing,'' in
compliance with Sec. 1.821(c) or (e); or
(ii) Any ``Computer Program Listing Appendix'' in compliance with
Sec. 1.96(c).
(3) Any submission of a ``Sequence Listing'' in electronic form of
300 MB-800 MB filed in an application under 35 U.S.C. 111 or 371 will
be subject to the fee set forth in Sec. 1.21(o)(1). Any submission of
a ``Sequence Listing'' filed in electronic form that exceeds 800 MB in
an application under 35 U.S.C. 111 or 371 will be subject to the fee
set forth in Sec. 1.21(o)(2).
0
3. Amend Sec. 1.58 by revising paragraphs (b) and (c) and adding
paragraphs (d) through (j) to read as follows:
Sec. 1.58 Chemical and mathematical formulas and tables.
* * * * *
(b) Chemical and mathematical formulas and tables must be presented
in compliance with Sec. 1.52(a) and (b), except that chemical and
mathematical formulas or tables may be placed in a landscape
orientation if they cannot be presented satisfactorily in a portrait
orientation. Typewritten characters used in such formulas and tables
must be chosen from a block (nonscript) type font or lettering style
having capital letters that should be at least 0.422 cm (0.166 inches)
high (e.g., preferably Arial, Times Roman, or Courier, with a font size
of 12 point), but may be no smaller than 0.21cm (0.08 inches) high
(e.g., a font size of 6 point). A space at least 0.64 cm (0.25 inches)
high should be provided between complex formulas and tables and the
text. Chemical and mathematical formulas must be configured to maintain
the proper positioning of their characters when displayed in order to
preserve their intended meaning. Tables should have the lines and
columns of data closely spaced to conserve space, consistent with a
high degree of legibility.
(c) The following ``Large Tables'' may be submitted in electronic
form in ASCII plain text via the USPTO patent electronic filing system
or on a read-only optical disc, in compliance with Sec. 1.52(e),
excluding an international application during the international stage:
(1) Any individual table that is more than 50 pages in length; or
(2) Multiple tables, if the total number of pages of all the tables
in an
[[Page 28312]]
application exceeds 100 pages in length, where a table page is a page
printed on paper, in conformance with paragraph (b) of this section.
(d) ``Large Tables'' submitted in electronic form in ASCII plain
text must conform to the following requirements:
(1) Must maintain the spatial relationships (e.g., alignment of
columns and rows) of the table elements when displayed to visually
preserve the relational information they convey.
(2) Must have the following compatibilities:
(i) Computer compatibility: PC or Mac[supreg];
(ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg].
(3) Must be in ASCII plain text, where:
(i) All printable characters (including the space character) are
permitted;
(ii) No nonprintable (ASCII control) characters are permitted,
except ASCII Carriage Return plus ASCII Line Feed (CRLF) or Line Feed
(LF) as line terminators.
(4) Must be named as *.txt, where ``*'' is one character or a
combination of characters limited to upper- or lowercase letters,
numbers, hyphens, and underscores and does not exceed 60 characters in
total, excluding the extension. No spaces or other types of characters
are permitted in the file name.
(5) Must be incorporated by reference in a separate paragraph of
the specification, in accordance with Sec. 1.77(b)(5).
(e) ``Large Tables'' submitted via the USPTO patent electronic
filing system must not exceed 25 MB, and file compression is not
permitted.
(f) ``Large Tables'' submitted in compliance with Sec. 1.52(e) via
read-only optical disc, must meet the following requirements:
(1) The ASCII plain text file may be compressed using
WinZip[supreg], 7-Zip, or Unix[supreg]/Linux[supreg] Zip;
(2) A compressed file must not be self-extracting; and
(3) A compressed ASCII plain text file that does not fit on a
single read-only optical disc may be split into multiple file parts in
accordance with the target read-only optical disc size and labeled in
compliance with Sec. 1.52(e)(5)(vi).
(g) Any amendments to ``Large Tables'' in electronic form in ASCII
plain text format must include:
(1) A replacement ASCII plain text file, in accordance with the
requirements of paragraphs (d) through (f) of this section, submitted
via the USPTO patent electronic filing system or on a read-only optical
disc, in compliance with Sec. 1.52(e), labeled as ``REPLACEMENT MM/DD/
YYYY'' (with the month, day, and year of creation indicated);
(2) A request that the amendment be made by incorporation by
reference of the material in the replacement ASCII plain text file, in
a separate paragraph of the specification (replacing any prior such
paragraph, as applicable) identifying the name of the file, the date of
creation, and the size of the file in bytes (see Sec. 1.77(b)(5));
(3) A statement that identifies the location of all deletions,
replacements, or additions to the ASCII plain text file; and
(4) A statement that the replacement ASCII plain text file contains
no new matter.
(h) The specification of an application with ``Large Tables'' as an
ASCII plain text file, present on the application filing date, without
an incorporation by reference of the material contained in the ASCII
plain text file, must be amended to contain a separate paragraph
incorporating by reference the material contained in the ASCII plain
text file, in accordance with Sec. 1.77(b)(5).
(i) Any read-only optical disc for ``Large Tables'' must be
submitted in duplicate. The read-only optical disc and duplicate copy
must be labeled ``Copy 1'' and ``Copy 2,'' respectively. The
transmittal letter that accompanies the read-only optical discs must
include a statement that the two read-only optical discs are identical.
In the event that the two read-only optical discs are not identical,
the Office will use the read-only optical disc labeled ``Copy 1'' for
further processing.
(j) Any amendment to the information on a read-only optical disc
must be by way of a replacement read-only optical disc, in compliance
with Sec. 1.58(g), where the replacement read-only optical disc and
copy must be labeled ``COPY 1 REPLACEMENT MM/DD/YYYY'' (with the month,
day, and year of creation indicated), and ``COPY 2 REPLACEMENT MM/DD/
YYYY,'' respectively.
0
4. Amend Sec. 1.71 by revising paragraph (f) to read as follows:
Sec. 1.71 Detailed description and specification of the invention.
* * * * *
(f) The specification must commence on a separate sheet. Each sheet
including part of the specification may not include other parts of the
application or other information. The claim(s), abstract, and
``Sequence Listing'' (if required or submitted under Sec. 1.821(c))
should not be included on a sheet including any other part of the
application.
* * * * *
0
5. Amend Sec. 1.77 by revising paragraphs (b)(5) and (13) to read as
follows:
Sec. 1.77 Arrangement of application elements.
* * * * *
(b) * * *
(5) An incorporation by reference statement regarding the material
on the one or more ASCII plain text files, submitted via the USPTO
patent electronic filing system or on one or more read-only optical
discs (see Sec. 1.52(e)(8)), identifying the names of each file, the
date of creation of each file, and the size of each file in bytes, for
the following document types:
(i) A ``Computer Program Listing Appendix'' (see Sec. 1.96(c));
(ii) A ``Sequence Listing'' (see Sec. 1.821(c)); or
(iii) ``Large Tables'' (see Sec. 1.58(c)).
* * * * *
(13) ``Sequence Listing,'' required by Sec. 1.821(c), that is
submitted as a Portable Document Format (PDF) file (as set forth in
Sec. 1.821(c)(1)(ii)) via the USPTO patent electronic filing system or
on physical sheets of paper (as set forth in Sec. 1.821(c)(1)(iii)).
* * * * *
0
6. Amend Sec. 1.96 by revising paragraphs (a) and (c) to read as
follows:
Sec. 1.96 Submission of computer program listings.
(a) General. Descriptions of the operation and general content of
computer program listings should appear in the description portion of
the specification. A computer program listing for the purpose of this
section is defined as a document that lists in appropriate sequence the
instructions, routines, and other contents of a program for a computer.
The program listing may be either in machine or machine-independent
(object or source) language that will cause a computer to perform a
desired procedure or task such as solve a problem, regulate the flow of
work in a computer, or control or monitor events. Computer program
listings may be submitted in patent applications, as set forth in
paragraphs (b) and (c) of this section.
* * * * *
(c) As an appendix that will not be printed: Any computer program
listing may, and any computer program listing having over 300 lines (up
to 72 characters per line) must, be submitted as an electronic document
in ASCII plain text, whether submitted via the
[[Page 28313]]
USPTO patent electronic filing system or on a read-only optical disc,
in compliance with Sec. 1.52(e). An electronic document containing
such a computer program listing is to be referred to as a ``Computer
Program Listing Appendix.'' The ``Computer Program Listing Appendix''
will not be part of the printed patent. The specification must include
an incorporation by reference of the ``Computer Program Listing
Appendix,'' in accordance with Sec. 1.77(b)(5).
(1) A ``Computer Program Listing Appendix'' must conform to the
following requirements:
(i) Computer compatibility: PC or Mac[supreg];
(ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg];
(iii) Line terminator: ASCII CRLF or LF only; and
(iv) Control Codes: The data must not be dependent on control
characters or codes that are not defined in the ASCII character set.
(2) Each file must be named as *.txt, where ``*'' is one character
or a combination of characters limited to upper- or lowercase letters,
numbers, hyphens, and underscores and does not exceed 60 characters in
total, excluding the extension. No spaces or other types of characters
are permitted in the file name.
(3) Each file containing a ``Computer Program Listing Appendix''
submitted via the USPTO patent electronic filing system must not exceed
25 MB, and file compression is not permitted.
(4) A ``Computer Program Listing Appendix'' submitted in compliance
with Sec. 1.52(e) must conform to the following requirements:
(i) A separate read-only optical disc containing a ``Computer
Program Listing Appendix'' must be submitted for each applicable
application;
(ii) Multiple computer program listings for a single application
may be placed on a single read-only optical disc;
(iii) Multiple read-only optical discs, containing one or more
computer program listings, may be submitted for a single application,
if necessary;
(iv) Any computer program listing may, and a computer program
listing having a nested file structure must, when submitted in
compliance with Sec. 1.52(e), be compressed into a single file using
WinZip[supreg], 7-Zip, or Unix[supreg]/Linux[supreg] Zip;
(v) Any compressed file must not be self-extracting; and
(vi) A compressed ASCII plain text file that does not fit on a
single read-only optical disc may be split into multiple file parts, in
accordance with the target read-only optical disc size and labeled in
compliance with Sec. 1.52(e)(5)(vi).
(5) Any amendments to a ``Computer Program Listing Appendix'' in
electronic form in ASCII plain text format must include:
(i) A replacement ASCII plain text file, in accordance with the
requirements of paragraph (c) of this section, via the USPTO patent
electronic filing system, or on a read-only optical disc, in compliance
with Sec. 1.52(e) and labeled as ``COPY 1 REPLACEMENT MM/DD/YYYY''
(with the month, day, and year of creation indicated) and ``COPY 2
REPLACEMENT MM/DD/YYYY;''
(ii) A request that the amendment be made by incorporation by
reference of the material in the replacement ASCII plain text file, in
a separate paragraph of the specification (replacing any prior such
paragraph) identifying the name of the file, the date of creation, and
the size of the file in bytes (see Sec. 1.77(b)(5));
(iii) A statement that identifies the location of all deletions,
replacements, or additions to the ASCII plain text file; and
(iv) A statement that the replacement ASCII plain text file
contains no new matter.
(6) The specification of a complete application with a ``Computer
Program Listing Appendix'' as an ASCII plain text file, filed on the
application filing date, without an incorporation by reference of the
material contained in the ASCII plain text file, must be amended to
contain a separate paragraph incorporating by reference the material
contained in the ASCII plain text file, in accordance with Sec.
1.77(b)(5).
(7) Any read-only optical disc for a ``Computer Program Listing
Appendix'' must be submitted in duplicate. The read-only optical disc
and duplicate copy must be labeled ``Copy 1'' and ``Copy 2,''
respectively. The transmittal letter that accompanies the read-only
optical discs must include a statement that the two read-only optical
discs are identical. In the event that the two read-only optical discs
are not identical, the Office will use the read-only optical disc
labeled ``Copy 1'' for further processing. Any amendment to the
information on a read-only optical disc must be by way of a replacement
read-only optical disc, in compliance with Sec. 1.96(c)(5).
0
7. Amend Sec. 1.121 by revising paragraph (b) introductory text and
adding paragraph (b)(6) to read as follows:
Sec. 1.121 Manner of making amendments in applications.
* * * * *
(b) Specification. Amendments to the specification, other than the
claims, ``Large Tables (Sec. 1.58(c)), a ``Computer Program Listing
Appendix'' (Sec. 1.96(c)(5) and (7)), and a ``Sequence Listing'' or
CRF (Sec. 1.825), must be made by adding, deleting, or replacing a
paragraph; by replacing a section; or by a substitute specification, in
the manner specified in this section.
* * * * *
(6) Changes to ``Large Tables,'' a ``Computer Program Listing
Appendix,'' or a ``Sequence Listing'' must be made in accordance with
Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5) for a ``Computer
Program Listing Appendix,'' and Sec. 1.825 for a ``Sequence Listing.''
* * * * *
0
8. Amend Sec. 1.173 by revising paragraphs (b)(1) and (d) to read as
follows:
Sec. 1.173 Reissue specification, drawings, and amendments.
* * * * *
(b) * * *
(1) Specification other than the claims, ``Large Tables'' (Sec.
1.58(c)), a ``Computer Program Listing Appendix'' (Sec. 1.96(c)), or a
``Sequence Listing'' (Sec. 1.821(c)). (i) Changes to the
specification, other than to the claims, ``Large Tables'' (Sec.
1.58(c)), a ``Computer Program Listing Appendix'' (Sec. 1.96(c)), or a
``Sequence Listing'' (Sec. 1.821(c)), must be made by submission of
the entire text of an added or rewritten paragraph, including markings
pursuant to paragraph (d) of this section, except that an entire
paragraph may be deleted by a statement deleting the paragraph, without
presentation of the text of the paragraph. The precise point in the
specification where any added or rewritten paragraph is located must be
identified.
(ii) Changes to ``Large Tables,'' a ``Computer Program Listing
Appendix,'' or a ``Sequence Listing'' must be made in accordance with
Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5) for a ``Computer
Program Listing Appendix,'' and Sec. 1.825 for a ``Sequence Listing.''
* * * * *
(d) Changes shown by markings. Any changes relative to the patent
being reissued that are made to the specification, including the claims
but excluding ``Large Tables,'' a ``Computer Program Listing
Appendix,'' or a ``Sequence Listing,'' upon filing or by an amendment
paper in the reissue application, must include the following markings:
[[Page 28314]]
(1) The matter to be omitted by reissue must be enclosed in
brackets; and
(2) The matter to be added by reissue must be underlined.
* * * * *
0
9. Amend Sec. 1.530 by revising paragraph (d)(1) to read as follows:
Sec. 1.530 Statement by patent owner in ex parte reexamination;
amendment by patent owner in ex parte or inter partes reexamination;
inventorship change in ex parte or inter partes reexamination.
* * * * *
(d) * * *
(1) Specification other than the claims, ``Large Tables'' (Sec.
1.58(c)), a ``Computer Program Listing Appendix'' (Sec. 1.96(c)), or a
``Sequence Listing'' (Sec. 1.821(c)).
(i) Changes to the specification, other than to the claims, ``Large
Tables'' (Sec. 1.58(c)), a ``Computer Program Listing Appendix''
(Sec. 1.96(c)), or a ``Sequence Listing'' (Sec. 1.821(c)), must be
made by submission of the entire text of an added or rewritten
paragraph, including markings pursuant to paragraph (f) of this
section, except that an entire paragraph may be deleted by a statement
deleting the paragraph, without presentation of the text of the
paragraph. The precise point in the specification where any added or
rewritten paragraph is located must be identified.
(ii) Changes to ``Large Tables,'' a ``Computer Program Listing
Appendix,'' or a ``Sequence Listing'' must be made, in accordance with
Sec. 1.58(g) for ``Large Tables,'' Sec. 1.96(c)(5) for a ``Computer
Program Listing Appendix,'' and Sec. 1.825 for a ``Sequence Listing.''
* * * * *
0
10. Amend Sec. 1.821 by revising paragraphs (a), and (c) through (e),
removing and reserving paragraph (f), and revising paragraphs (g)
through (h) to read as follows:
Sec. 1.821 Nucleotide and/or amino acid sequence disclosures in
patent applications.
(a) Nucleotide and/or amino acid sequences, as used in Sec. Sec.
1.821 through 1.825, are interpreted to mean an unbranched sequence of
4 or more amino acids or an unbranched sequence of 10 or more
nucleotides. Branched sequences are specifically excluded from this
definition. Sequences with fewer than four specifically defined
nucleotides or amino acids are specifically excluded from this section.
``Specifically defined'' means those amino acids other than ``Xaa'' and
those nucleotide bases other than ``n,'' defined in accordance with
Appendices A through F to this subpart. Nucleotides and amino acids are
further defined as follows:
(1) Nucleotides: Nucleotides are intended to embrace only those
nucleotides that can be represented using the symbols set forth in
Appendix A to this subpart. Modifications (e.g., methylated bases) may
be described as set forth in Appendix B to this subpart, but shall not
be shown explicitly in the nucleotide sequence.
(2) Amino acids: Amino acids are those L-amino acids commonly found
in naturally occurring proteins and are listed in Appendix C to this
subpart. Those amino acid sequences containing D-amino acids are not
intended to be embraced by this definition. Any amino acid sequence
that contains post-translationally modified amino acids may be
described as the amino acid sequence that is initially translated using
the symbols shown in Appendix C to this subpart with the modified
positions (e.g., hydroxylations or glycosylations) being described as
set forth in Appendix D to this subpart, but these modifications shall
not be shown explicitly in the amino acid sequence. Any peptide or
protein that can be expressed as a sequence using the symbols in
Appendix C to this subpart, in conjunction with a description in the
Feature section, to describe, for example, modified linkages, cross
links and end caps, non-peptidyl bonds, etc., is embraced by this
definition.
Note 1 to paragraph (a): Appendices A through F contain Tables
1-6 of the World Intellectual Property Organization (WIPO) Handbook
on Industrial Property Information and Documentation, Standard
ST.25: Standard for the Presentation of Nucleotide and Amino Acid
Sequence Listings in Patent Applications (2009).
* * * * *
(c) Patent applications that contain disclosures of nucleotide and/
or amino acid sequences, as defined in paragraph (a) of this section,
must contain a ``Sequence Listing'' as a separate part of the
specification containing each of those nucleotide and/or amino acid
sequences and associated information using the symbols and format in
accordance with the requirements of Sec. Sec. 1.822 and 1.823. The
``Sequence Listing'' must be submitted as follows, except for a
national stage entry under Sec. 1.495(b)(1), where the ``Sequence
Listing'' has been previously communicated by the International Bureau
or originally filed in the United States Patent and Trademark Office
and complies with Patent Cooperation Treaty (PCT) Rule 5.2:
(1) As an ASCII plain text file, in compliance with Sec. 1.824,
submitted via the USPTO patent electronic filing system or on a read-
only optical disc under Sec. 1.52(e), accompanied by an incorporation
by reference statement of the ASCII plain text file, in a separate
paragraph of the specification, in accordance with Sec. 1.77(b)(5);
(2) As a PDF file via the USPTO patent electronic filing system; or
(3) On physical sheets of paper.
(d) Where the description or claims of a patent application discuss
a sequence that is set forth in the ``Sequence Listing,'' in accordance
with paragraph (c) of this section, reference must be made to the
sequence by use of a sequence identifier (Sec. 1.823(a)(5)), preceded
by ``SEQ ID NO:'' In the text of the description or claims, even if the
sequence is also embedded in the text of the description or claims of
the patent application. Where a sequence is presented in a drawing,
reference must be made to the sequence by use of the sequence
identifier (Sec. 1.823(a)(5)), either in the drawing or in the Brief
Description of the Drawings, where the correlation between multiple
sequences in the drawing and their sequence identifiers (Sec.
1.823(a)(5)) in the Brief Description is clear.
(e)(1) If the ``Sequence Listing'' under paragraph (c) is submitted
in an application filed under 35 U.S.C. 111(a) as a PDF file (Sec.
1.821(c)(2)) via the USPTO patent electronic filing system or on
physical sheets of paper (Sec. 1.821(c)(3)), then the following must
be submitted:
(i) A CRF of the ``Sequence Listing,'' in accordance with the
requirements of Sec. 1.824; and
(ii) A statement that the sequence information contained in the CRF
submitted under paragraph (e)(1)(i) of this section is identical to the
sequence information contained in the ``Sequence Listing'' under
paragraph (c) of this section.
(2) If the ``Sequence Listing'' under paragraph (c) of this section
in an application submitted under 35 U.S.C. 371 is a PDF file (Sec.
1.821(c)(2)) or on physical sheets of paper (Sec. 1.821(c)(3)), and
not also as an ASCII plain text file, in compliance with Sec. 1.824
(Sec. 1.821(c)(1)), then the following must be submitted:
(i) A CRF of the ``Sequence Listing,'' in accordance with the
requirements of Sec. 1.824; and
(ii) A statement that the sequence information contained in the CRF
submitted under paragraph (e)(2)(i) of this section is identical to the
sequence information contained in the ``Sequence Listing'' under
paragraph (c)(2) or (3) of this section.
[[Page 28315]]
(3) If a ``Sequence Listing'' in ASCII plain text format, in
compliance with Sec. 1.824, has not been submitted for an
international application under the PCT, and that application contains
disclosures of nucleotide and/or amino acid sequences, as defined in
paragraph (a) of this section, and is to be searched by the United
States International Searching Authority or examined by the United
States International Preliminary Examining Authority, then the
following must be submitted:
(i) A CRF of the ``Sequence Listing,'' in accordance with the
requirements of Sec. 1.824;
(ii) The late furnishing fee for providing a ``Sequence Listing''
in response to an invitation, as set forth in Sec. 1.445(a)(5); and
(iii) A statement that the sequence information contained in the
CRF, submitted under paragraph (e)(3)(i) of this section, does not go
beyond the disclosure in the international application as filed, or a
statement that the information recorded in the ASCII plain text file,
submitted under paragraph (e)(3)(i) of this section, is identical to
the sequence listing contained in the international application as
filed, as applicable.
(4) The CRF may not be retained as a part of the patent application
file.
(f) [Reserved]
(g) If any of the requirements of paragraphs (b) through (e) of
this section are not satisfied at the time of filing under 35 U.S.C.
111(a) or at the time of entering the national stage under 35 U.S.C.
371, the applicant will be notified and given a period of time within
which to comply with such requirements in order to prevent abandonment
of the application. Any amendment to add or replace a ``Sequence
Listing'' and CRF copy thereof in reply to a requirement under this
paragraph must be submitted in accordance with the requirements of
Sec. 1.825.
(h) If any of the requirements of paragraph (e)(3) of this section
are not satisfied at the time of filing an international application
under the PCT, and the application is to be searched by the United
States International Searching Authority or examined by the United
States International Preliminary Examining Authority, the applicant may
be sent a notice necessitating compliance with the requirements within
a prescribed time period. Where a ``Sequence Listing'' under PCT Rule
13ter is provided in reply to a requirement under this paragraph, it
must be accompanied by a statement that the information recorded in the
ASCII plain text file under paragraph (e)(3)(i) of this section is
identical to the sequence listing contained in the international
application as filed, or does not go beyond the disclosure in the
international application as filed, as applicable. It must also be
accompanied by the late furnishing fee, as set forth in Sec.
1.445(a)(5). If the applicant fails to timely provide the required CRF,
the United States International Searching Authority shall search only
to the extent that a meaningful search can be performed without the
CRF, and the United States International Preliminary Examining
Authority shall examine only to the extent that a meaningful
examination can be performed without the CRF.
0
11. Amend Sec. 1.822 by revising paragraphs (b), (c)(1), (3), (5) and
(6), (d)(1), (3) through (5), and (e) to read as follows:
Sec. 1.822 Symbols and format to be used for nucleotide and/or amino
acid sequence data.
* * * * *
(b) The code for representing the nucleotide and/or amino acid
sequence characters shall conform to the code set forth in Appendices A
and C to this subpart. No code other than that specified in these
sections shall be used in nucleotide and amino acid sequences. A
modified base or modified or unusual amino acid may be presented in a
given sequence as the corresponding unmodified base or amino acid if
the modified base or modified or unusual amino acid is one of those
listed in Appendices B and D to this subpart, and the modification is
also set forth in the Feature section. Otherwise, each occurrence of a
base or amino acid not appearing in Appendices A and C, shall be listed
in a given sequence as ``n'' or ``Xaa,'' respectively, with further
information, as appropriate, given in the Feature section, by including
one or more feature keys listed in Appendices E and F to this subpart.
Note 1 to paragraph (b): Appendices A through F contain Tables
1-6 of the World Intellectual Property Organization (WIPO) Handbook
on Industrial Property Information and Documentation, Standard
ST.25: Standard for the Presentation of Nucleotide and Amino Acid
Sequence Listings in Patent Applications (2009).
(c) * * *
(1) A nucleotide sequence shall be listed using the lowercase
letter for representing the one-letter code for the nucleotide bases
set forth in Appendix A to this subpart.
* * * * *
(3) The bases in the coding parts of a nucleotide sequence shall be
listed as triplets (codons). The amino acids corresponding to the
codons in the coding parts of a nucleotide sequence shall be listed
immediately below the corresponding codons. Where a codon spans an
intron, the amino acid symbol shall be listed below the portion of the
codon containing two nucleotides.
* * * * *
(5) A nucleotide sequence shall be represented, only by a single
strand, in the 5 to 3 direction, from left to right.
(6) The enumeration of nucleotide bases shall start at the first
base of the sequence with number 1. The enumeration shall be continuous
through the whole sequence in the direction 5 to 3. The enumeration
shall appear in the right margin, next to the line containing the one-
letter codes for the bases, and giving the number of the last base of
that line.
* * * * *
Note 2 to paragraph (c): Appendices A through F contain Tables
1-6 of the World Intellectual Property Organization (WIPO) Handbook
on Industrial Property Information and Documentation, Standard
ST.25: Standard for the Presentation of Nucleotide and Amino Acid
Sequence Listings in Patent Applications (2009).
(d) * * *
(1) The amino acids in a protein or peptide sequence shall be
listed using the three-letter abbreviation, with the first letter as an
uppercase character, as in Appendix C to this subpart.
* * * * *
(3) An amino acid sequence shall be represented in the amino to
carboxy direction, from left to right, and the amino and carboxy groups
shall not be represented in the sequence.
(4) The enumeration of amino acids may start at the first amino
acid of the first mature protein, with the number 1. When represented,
the amino acids preceding the mature protein (e.g., pre-sequences, pro-
sequences, pre-pro-sequences and signal sequences) shall have negative
numbers, counting backwards starting with the amino acid next to number
1. Otherwise, the enumeration of amino acids shall start at the first
amino acid at the amino terminal as number 1, and shall appear below
every 5 amino acids of the sequence. The enumeration method for amino
acid sequences that is set forth in this section remains applicable for
amino acid sequences that are circular in configuration, with the
exception that the designation of the first amino acid of the sequence
may be made at the option of the applicant.
(5) An amino acid sequence that contains internal terminator
symbols (e.g., ``Ter,'' ``*,'' or ``.,'' etc.) may not be
[[Page 28316]]
represented as a single amino acid sequence but shall be represented as
separate amino acid sequences.
Note 3 to paragraph (d): Appendices A through F contain Tables
1--6 of the World Intellectual Property Organization (WIPO) Handbook
on Industrial Property Information and Documentation, Standard
ST.25: Standard for the Presentation of Nucleotide and Amino Acid
Sequence Listings in Patent Applications (2009).
(e) A sequence with a gap or gaps shall be represented as a
plurality of separate sequences, with separate sequence identifiers
(Sec. 1.823(a)(5)), with the number of separate sequences being equal
in number to the number of continuous strings of sequence data. A
sequence composed of one or more noncontiguous segments of a larger
sequence or segments from different sequences shall be presented as a
separate sequence.
0
12. Revise Sec. 1.823 to read as follows:
Sec. 1.823 Requirements for content of a ``Sequence Listing'' part of
the specification.
(a) The ``Sequence Listing'' must comply with the following:
(1) The order and presentation of the items of information in the
``Sequence Listing'' shall conform to the arrangement in Appendix G.
The submission of those items of information designated with an ``M''
is mandatory. The submission of those items of information designated
with an ``O'' is optional.
(2) Each item of information shall begin on a new line with the
numeric identifier enclosed in angle brackets, as shown in Appendix G.
(3) Set forth numeric identifiers <110> through <170> at the
beginning of the ``Sequence Listing.''
(4) Include each disclosed nucleotide and/or amino acid sequence,
as defined in Sec. 1.821(a).
(5) Assign each sequence with a separate sequence identifier,
beginning with 1 and increasing sequentially by integers, and include
the sequence identifier in numeric identifier <210>.
(6) Use the code ``000'' in place of the sequence where no sequence
is present for a sequence identifier.
(7) Include the total number of SEQ ID NOs in numeric identifier
<160>, as defined in Appendix G, whether followed by a sequence or by
the code ``000.''
(8) Must not contain more than 74 characters per line.
(b)(1) Unless paragraph (b)(2) of this section applies, if the
``Sequence Listing'' required by Sec. 1.821(c) is submitted as an
ASCII plain text file via the USPTO patent electronic filing system or
on a read-only optical disc, in compliance with Sec. 1.52(e), then the
specification must contain a statement in a separate paragraph (see
Sec. 1.77(b)(5)) that incorporates by reference the material in the
ASCII plain text file identifying:
(i) The name of the file;
(ii) The date of creation; and
(iii) The size of the file in bytes.
(2) If the ``Sequence Listing'' required by Sec. 1.821(c) is
submitted as an ASCII plain text file via the USPTO patent electronic
filing system or on a read-only optical disc, in compliance with Sec.
1.52(e) for an international application during the international
stage, then incorporation by reference of the material in the ASCII
plain text file is not required.
(3) A ``Sequence Listing'' required by Sec. 1.821(c) that is
submitted as a PDF file (Sec. 1.821(c)(2)) via the USPTO patent
electronic filing system or on physical sheets of paper (Sec.
1.821(c)(3)), setting forth the nucleotide and/or amino acid sequence
and associated information in accordance with paragraph (a) of this
section:
(i) Must begin on a new page;
(ii) Must be titled ``Sequence Listing'';
(iii) Must not include material other than the ``Sequence Listing''
itself;
(iv) Must have sheets containing no more than 66 lines, with each
line containing no more than 74 characters;
(v) Should have sheets numbered independently of the numbering of
the remainder of the application; and
(vi) Should use a fixed-width font exclusively throughout.
0
13. Revise Sec. 1.824 to read as follows:
Sec. 1.824 Form and format for a nucleotide and/or amino acid
sequence submission as an ASCII plain text file.
(a) A ``Sequence Listing'' under Sec. 1.821(c)(1) and the CRF
required by Sec. 1.821(e) submitted as an ASCII plain text file may be
created by any means, such as text editors, nucleotide/amino acid
sequence editors, or other custom computer programs; however, the ASCII
plain text file must conform to the following requirements:
(1) Must have the following compatibilities:
(i) Computer compatibility: PC or Mac[supreg];
(ii) Operating system compatibility: MS-DOS[supreg], MS-
Windows[supreg], Mac OS[supreg], or Unix[supreg]/Linux[supreg].
(2) Must be in ASCII plain text, where:
(i) All printable characters (including the space character) are
permitted;
(ii) No nonprintable (ASCII control) characters are permitted,
except ASCII CRLF or LF as line terminators.
(3) Must be named as *.txt, where ``*'' is one character or a
combination of characters limited to upper- or lowercase letters,
numbers, hyphens, and underscores and does not exceed 60 characters in
total, excluding the extension. No spaces or other types of characters
are permitted in the file name.
(4) Must contain no more than 74 printable characters in each line.
(5) Pagination is not permitted; the ASCII plain text file must be
one continuous file, with no ``hard page break'' codes and no page
numbering.
(b) The ASCII plain text file must contain a copy of a single
``Sequence Listing'' in a single file and be submitted either:
(1) Electronically via the USPTO patent electronic filing system,
where the file must not exceed 100 MB, and file compression is not
permitted; or
(2) On read-only optical disc(s) in compliance with Sec. 1.52(e),
where:
(i) A file that is not compressed must be contained on a single
read-only optical disc;
(ii) The file may be compressed using WinZip[supreg], 7-Zip, or
Unix[supreg]/Linux[supreg] Zip;
(iii) A compressed file must not be self-extracting; and
(iv) A compressed ASCII plain text file that does not fit on a
single read-only optical disc may be split into multiple file parts, in
accordance with the target read-only optical disc size, and labeled in
compliance with 1.52(e)(5)(vi).
0
14. Revise Sec. 1.825 to read as follows:
Sec. 1.825 Amendment to add or replace a ``Sequence Listing'' and CRF
copy thereof.
(a) Any amendment adding a ``Sequence Listing'' (Sec. 1.821(c))
after the application filing date must include:
(1) A ``Sequence Listing,'' in accordance with the requirements of
Sec. Sec. 1.821 through 1.824, submitted as:
(i) An ASCII plain text file under Sec. 1.821(c)(1) via the USPTO
patent electronic filing system or on a read-only optical disc, in
compliance with Sec. 1.52(e);
(ii) PDF file via the USPTO patent electronic filing system; or
(iii) Physical sheets of paper;
(2) A request that the amendment be made:
(i) By incorporation by reference of the material in the ASCII
plain text file, in a separate paragraph of the specification,
identifying the name of the file, the date of creation, and the size of
the file in bytes (see Sec. 1.77(b)(5)), for a ``Sequence Listing''
submitted under Sec. 1.821(c)(1), except when submitted to the United
States International Preliminary Examining Authority for an
international application; or
(ii) By inserting, after the abstract of the disclosure, a
``Sequence Listing''
[[Page 28317]]
submitted as a PDF file under Sec. 1.821(c)(2) or submitted on
physical sheets of paper under Sec. 1.821(c)(3), except when submitted
to the United States International Preliminary Examining Authority for
an international application;
(3) A statement that indicates the basis for the amendment, with
specific references to particular parts of the application
(specification, claims, drawings) for all sequence data in the
``Sequence Listing'' in the application as originally filed;
(4) A statement that the ``Sequence Listing'' includes no new
matter;
(5) A new or substitute CRF under Sec. 1.821(e), if:
(i) The added ``Sequence Listing'' is submitted as a PDF file,
under Sec. 1.821(c)(2), or on physical sheets of paper, under Sec.
1.821(c)(3); and
(ii) A CRF, under Sec. 1.821(e), was not submitted, not compliant
with Sec. 1.824, or not the same as the ``Sequence Listing''; and
(6) A statement that the sequence information contained in the CRF
is the same as the sequence information contained in the added
``Sequence Listing,'' if submitted as a PDF file, under Sec.
1.821(c)(2), or on physical sheets of paper, under Sec. 1.821(c)(3).
(b) Any amendment to a ``Sequence Listing'' (Sec. 1.821(c)) must
include:
(1) A replacement ``Sequence Listing,'' in accordance with the
requirements of Sec. Sec. 1.821 through 1.824, submitted as:
(i) An ASCII plain text file under Sec. 1.821(c)(1) via the USPTO
patent electronic filing system, or on a read-only optical disc, in
compliance with Sec. 1.52(e), labeled as ``REPLACEMENT MM/DD/YYYY''
(with the month, day, and year of creation indicated);
(ii) A PDF file via the USPTO patent electronic filing system; or
(iii) Physical sheets of paper;
(2) A request that the amendment be made:
(i) By incorporation by reference of the material in the ASCII
plain text file, in a separate paragraph of the specification
(replacing any prior such paragraph, as applicable) identifying the
name of the file, the date of creation, and the size of the file in
bytes (see Sec. 1.77(b)(5)) for a ``Sequence Listing'' under Sec.
1.821(c)(1), except when submitted to the United States International
Preliminary Examining Authority for an international application; or
(ii) By placing, after the abstract of the disclosure, a ``Sequence
Listing'' submitted as a PDF file, under Sec. 1.821(c)(2), or on
physical sheets of paper, under Sec. 1.821(c)(3) (replacing any prior
``Sequence Listing,'' as applicable), except when submitted to the
United States International Preliminary Examining Authority for an
international application;
(3) A statement that identifies the location of all deletions,
replacements, or additions to the ``Sequence Listing'';
(4) A statement that indicates the basis for the amendment, with
specific references to particular parts of the application
(specification, claims, drawings) as originally filed for all amended
sequence data in the replacement ``Sequence Listing'';
(5) A statement that the replacement ``Sequence Listing'' includes
no new matter;
(6) A new or substitute CRF under Sec. 1.821(e) with the amendment
incorporated therein, if:
(i) The replacement ``Sequence Listing'' is submitted as a PDF
file, under Sec. 1.821(c)(2), or on physical sheets of paper, under
Sec. 1.821(c)(3); and
(ii) A CRF, under Sec. 1.821(e), was not submitted, not compliant
with Sec. 1.824, or not the same as the submitted ``Sequence
Listing''; and
(7) A statement that the sequence information contained in the CRF
is the same as the sequence information contained in the replacement
``Sequence Listing'' when submitted as a PDF file, under Sec.
1.821(c)(2), or on physical sheets of paper, under Sec. 1.821(c)(3).
(c) The specification of a complete application, filed on the
application filing date, with a ``Sequence Listing'' as an ASCII plain
text file, under Sec. 1.821(c)(1), without an incorporation by
reference of the material contained in the ASCII plain text file, must
be amended to contain a separate paragraph incorporating by reference
the material contained in the ASCII plain text file, in accordance with
Sec. 1.77(b)(5), except for international applications during the
international stage or national stage.
(d) Any appropriate amendments to the ``Sequence Listing'' in a
patent (e.g., by reason of reissue, reexamination, or certificate of
correction) must comply with the requirements of paragraph (b) of this
section.
0
15. Redesignate the appendix to subpart G of part 1 as appendix G, add
appendices A through F, and revise newly redesignated appendix G as
follows:
Appendices A Through G of Subpart G of Part 1
Appendix A: List of Nucleotides
Source: World Intellectual Property Organization (WIPO) Handbook
on Industrial Property Information and Documentation, Standard
ST.25: Standard for the Presentation of Nucleotide and Amino Acid
Sequence Listings in Patent Applications (2009)
------------------------------------------------------------------------
Origin of
Symbol Meaning designation
------------------------------------------------------------------------
a............................... a................. adenine.
g............................... g................. guanine.
c............................... c................. cytosine.
t............................... t................. thymine.
u............................... u................. uracil.
r............................... g or a............ purine
y............................... t/u or c.......... pyrimidine.
m............................... a or c............ amino.
k............................... g or t/u.......... keto.
s............................... g or c............ strong
interactions 3H-
bonds.
w............................... a or t/u.......... weak interactions
2H-bonds.
b............................... g or c or t/u..... not a.
d............................... a or g or t/u..... not c.
h............................... a or c or t/u..... not g.
v............................... a or g or c....... not t, not u.
n............................... a or g or c or t/ any
u, unknown, or
other.
------------------------------------------------------------------------
[[Page 28318]]
Appendix B: List of Modified Nucleotides
Source: World Intellectual Property Organization (WIPO) Handbook
on Industrial Property Information and Documentation, Standard
ST.25: Standard for the Presentation of Nucleotide and Amino Acid
Sequence Listings in Patent Applications (2009)
------------------------------------------------------------------------
Symbol Meaning
------------------------------------------------------------------------
ac4c.............................. 4-acetylcytidine.
chm5u............................. 5-(carboxyhydroxymethyl)uridine.
cm................................ 2'-O-methylcytidine.
cmnm5s2u.......................... 5-carboxymethylaminomethyl-2-
thiouridine.
cmnm5u............................ 5-carboxymethylaminomethyluridine.
d................................. dihydrouridine.
fm................................ 2'-O-methylpseudouridine.
gal q............................. beta, D-galactosylqueuosine.
gm................................ 2'-O-methylguanosine.
i................................. inosine.
i6a............................... N6-isopentenyladenosine.
m1a............................... 1-methyladenosine.
m1f............................... 1-methylpseudouridine.
m1g............................... 1-methylguanosine.
m1i............................... 1-methylinosine.
m22g.............................. 2,2-dimethylguanosine.
m2a............................... 2-methyladenosine.
m2g............................... 2-methylguanosine.
m3c............................... 3-methylcytidine.
m5c............................... 5-methylcytidine.
m6a............................... N6-methyladenosine.
m7g............................... 7-methylguanosine.
mam5u............................. 5-methylaminomethyluridine.
mam5s2u........................... 5-methoxyaminomethyl-2-thiouridine.
man q............................. beta, D-mannosylqueuosine.
mcm5s2u........................... 5-methoxycarbonylmethyl-2-
thiouridine.
mcm5u............................. 5-methoxycarbonylmethyluridine.
mo5u.............................. 5-methoxyuridine.
ms2i6a............................ 2-methylthio-N6-
isopentenyladenosine.
ms2t6a............................ N-((9-beta-D-ribofuranosyl-2-
methylthiopurine-6-
yl)carbamoyl)threonine.
mt6a.............................. N-((9-beta-D-ribofuranosylpurine-6-
yl)N-methylcarbamoyl)threonine.
mv................................ uridine-5-oxyacetic acid-
methylester.
o5u............................... uridine-5-oxyacetic acid.
osyw.............................. wybutoxosine.
p................................. pseudouridine.
q................................. queuosine.
s2c............................... 2-thiocytidine.
s2t............................... 5-methyl-2-thiouridine.
s2u............................... 2-thiouridine.
s4u............................... 4-thiouridine.
t................................. 5-methyluridine.
t6a............................... N-((9-beta-D-ribofuranosylpurine-6-
yl)-carbamoyl)threonine.
tm................................ 2'-O-methyl-5-methyluridine.
um................................ 2'-O-methyluridine.
yw................................ wybutosine.
x................................. 3-(3-amino-3-carboxy-propyl)uridine,
(acp3)u.
------------------------------------------------------------------------
Appendix C: List of Amino Acids
Source: World Intellectual Property Organization (WIPO) Handbook
on Industrial Property Information and Documentation, Standard
ST.25: Standard for the Presentation of Nucleotide and Amino Acid
Sequence Listings in Patent Applications (2009)
------------------------------------------------------------------------
Symbol Meaning
------------------------------------------------------------------------
Ala....................................... Alanine.
Cys....................................... Cysteine.
Asp....................................... Aspartic Acid.
Glu....................................... Glutamic Acid.
Phe....................................... Phenylalanine.
Gly....................................... Glycine.
His....................................... Histidine.
Ile....................................... Isoleucine.
Lys....................................... Lysine.
Leu....................................... Leucine.
Met....................................... Methionine.
Asn....................................... Asparagine.
Pro....................................... Proline.
Gln....................................... Glutamine.
Arg....................................... Arginine.
Ser....................................... Serine.
Thr....................................... Threonine.
Val....................................... Valine.
Trp....................................... Tryptophan.
Tyr....................................... Tyrosine.
Asx....................................... Asp or Asn.
Glx....................................... Glu or Gln.
Xaa....................................... unknown or other.
------------------------------------------------------------------------
Appendix D: List of Modified and Unusual Amino Acids
Source: World Intellectual Property Organization (WIPO) Handbook
on Industrial Property Information and Documentation, Standard
ST.25: Standard for the Presentation of Nucleotide and Amino Acid
Sequence Listings in Patent Applications (2009)
------------------------------------------------------------------------
Symbol Meaning
------------------------------------------------------------------------
Aad....................................... 2-Aminoadipic acid.
bAad...................................... 3-Aminoadipic acid.
bAla...................................... beta-Alanine, beta-
Aminopropionic acid.
Abu....................................... 2-Aminobutyric acid.
[[Page 28319]]
4Abu...................................... 4-Aminobutyric acid,
piperidinic acid.
Acp....................................... 6-Aminocaproic acid.
Ahe....................................... 2-Aminoheptanoic acid.
Aib....................................... 2-Aminoisobutyric acid.
bAib...................................... 3-Aminoisobutyric acid.
Apm....................................... 2-Aminopimelic acid.
Dbu....................................... 2,4 Diaminobutyric acid.
Des....................................... Desmosine.
Dpm....................................... 2,2'-Diaminopimelic acid.
Dpr....................................... 2,3-Diaminopropionic acid.
EtGly..................................... N-Ethylglycine.
EtAsn..................................... N-Ethylasparagine.
Hyl....................................... Hydroxylysine.
aHyl...................................... allo-Hydroxylysine.
3Hyp...................................... 3-Hydroxyproline.
4Hyp...................................... 4-Hydroxyproline.
Ide....................................... Isodesmosine.
aIle...................................... allo-Isoleucine.
MeGly..................................... N-Methylglycine, sarcosine.
MeIle..................................... N-Methylisoleucine.
MeLys..................................... 6-N-Methyllysine.
MeVal..................................... N-Methylvaline.
Nva....................................... Norvaline.
Nle....................................... Norleucine.
Orn....................................... Ornithine.
------------------------------------------------------------------------
Appendix E: List of Feature Keys Related to Nucleotide Sequences
Source: World Intellectual Property Organization (WIPO) Handbook
on Industrial Property Information and Documentation, Standard
ST.25: Standard for the Presentation of Nucleotide and Amino Acid
Sequence Listings in Patent Applications (2009)
------------------------------------------------------------------------
Key Description
------------------------------------------------------------------------
allele....................... a related individual or strain contains
stable, alternative forms of the same
gene, which differs from the presented
sequence at this location (and perhaps
others).
attenuator................... (1) region of DNA at which regulation of
termination of transcription occurs,
which controls the expression of some
bacterial operons; (2) sequence segment
located between the promoter and the
first structural gene that causes
partial termination of transcription.
C_region..................... constant region of immunoglobulin light
and heavy chains, and T-cell receptor
alpha, beta, and gamma chains; includes
one or more exons depending on the
particular chain.
CAAT_signal.................. CAAT box; part of a conserved sequence
located about 75 bp upstream of the
start point of eukaryotic transcription
units which may be involved in RNA
polymerase binding; consensus=GG (C or
T) CAATCT.
CDS.......................... coding sequence; sequence of nucleotides
that corresponds with the sequence of
amino acids in a protein (location
includes stop codon); feature includes
amino acid conceptual translation.
conflict..................... independent determinations of the
``same'' sequence differ at this site or
region.
D-loop....................... displacement loop; a region within
mitochondrial DNA in which a short
stretch of RNA is paired with one strand
of DNA, displacing the original partner
DNA strand in this region; also used to
describe the displacement of a region of
one strand of duplex DNA by a single
stranded invader in the reaction
catalyzed by RecA protein.
D-segment.................... diversity segment of immunoglobulin heavy
chain, and T-cell receptor beta chain.
enhancer..................... a cis-acting sequence that increases the
utilization of (some) eukaryotic
promoters, and can function in either
orientation and in any location
(upstream or downstream) relative to the
promoter.
exon......................... region of genome that codes for portion
of spliced mRNA; may contain 5'UTR, all
CDSs, and 3'UTR.
GC_signal.................... GC box; a conserved GC-rich region
located upstream of the start point of
eukaryotic transcription units which may
occur in multiple copies or in either
orientation; consensus=GGGCGG.
gene......................... region of biological interest identified
as a gene and for which a name has been
assigned.
iDNA......................... intervening DNA; DNA which is eliminated
through any of several kinds of
recombination.
intron....................... a segment of DNA that is transcribed, but
removed from within the transcript by
splicing together the sequences (exons)
on either side of it.
J_segment.................... joining segment of immunoglobulin light
and heavy chains, and T-cell receptor
alpha, beta, and gamma chains.
LTR.......................... long terminal repeat, a sequence directly
repeated at both ends of a defined
sequence, of the sort typically found in
retroviruses.
mat_peptide.................. mature peptide or protein coding
sequence; coding sequence for the mature
or final peptide or protein product
following post-translational
modification; the location does not
include the stop codon (unlike the
corresponding CDS).
misc_binding................. site in nucleic acid which covalently or
non-covalently binds another moiety that
cannot be described by any other Binding
key (primer_bind or protein_bind).
misc_difference.............. feature sequence is different from that
presented in the entry and cannot be
described by any other Difference key
(conflict, unsure, old_sequence,
mutation, variation, allele, or
modified_base).
misc_feature................. region of biological interest which
cannot be described by any other feature
key; a new or rare feature.
misc_recomb.................. site of any generalized, site-specific or
replicative recombination event where
there is a breakage and reunion of
duplex DNA that cannot be described by
other recombination keys (iDNA and
virion) or qualifiers of source key (/
insertion_seq, /transposon, /proviral).
misc_RNA..................... any transcript or RNA product that cannot
be defined by other RNA keys
(prim_transcript, precursor_RNA, mRNA,
5'clip, 3'clip, 5'UTR, 3'UTR, exon, CDS,
sig_peptide, transit_peptide,
mat_peptide, intron, polyA_site, rRNA,
tRNA, scRNA, and snRNA).
misc_signal.................. any region containing a signal
controlling or altering gene function or
expression that cannot be described by
other Signal keys (promoter,
CAAT_signal, TATA_signal, -35_signal, -
10_signal, GC_signal, RBS, polyA_signal,
enhancer, attenuator, terminator, and
rep_origin).
misc_structure............... any secondary or tertiary structure or
conformation that cannot be described by
other Structure keys (stem_loop and D-
loop).
modified_base................ the indicated nucleotide is a modified
nucleotide and should be substituted for
by the indicated molecule (given in the
mod_base qualifier value).
mRNA......................... messenger RNA; includes 5' untranslated
region (5'UTR), coding sequences (CDS,
exon) and 3' untranslated region
(3'UTR).
mutation..................... a related strain has an abrupt,
inheritable change in the sequence at
this location.
N_region..................... extra nucleotides inserted between
rearranged immunoglobulin segments.
old_sequence................. the presented sequence revises a previous
version of the sequence at this
location.
polyA_signal................. recognition region necessary for
endonuclease cleavage of an RNA
transcript that is followed by
polyadenylation; consensus=AATAAA.
polyA_site................... site on an RNA transcript to which will
be added adenine residues by post-
transcriptional polyadenylation.
[[Page 28320]]
precursor_RNA................ any RNA species that is not yet the
mature RNA product; may include 5'
clipped region (5'clip), 5' untranslated
region (5'UTR), coding sequences (CDS,
exon), intervening sequences (intron),
3' untranslated region (3'UTR), and 3'
clipped region (3'clip).
prim_transcript.............. primary (initial, unprocessed)
transcript; includes 5' clipped region
(5'clip), 5' untranslated region
(5'UTR), coding sequences (CDS, exon),
intervening sequences (intron), 3'
untranslated region (3'UTR), and 3'
clipped region (3'clip).
primer_bind.................. non-covalent primer binding site for
initiation of replication,
transcription, or reverse transcription;
includes site(s) for synthetic, for
example, PCR primer elements.
promoter..................... region on a DNA molecule involved in RNA
polymerase binding to initiate
transcription.
protein_bind................. non-covalent protein binding site on
nucleic acid.
RBS.......................... ribosome binding site.
repeat_region................ region of genome containing repeating
units.
repeat_unit.................. single repeat element.
rep_origin................... origin of replication; starting site for
duplication of nucleic acid to give two
identical copies.
rRNA......................... mature ribosomal RNA; the RNA component
of the ribonucleoprotein particle
(ribosome) which assembles amino acids
into proteins.
S_region..................... switch region of immunoglobulin heavy
chains; involved in the rearrangement of
heavy chain DNA leading to the
expression of a different immunoglobulin
class from the same B-cell.
satellite.................... many tandem repeats (identical or
related) of a short basic repeating
unit; many have a base composition or
other property different from the genome
average that allows them to be separated
from the bulk (main band) genomic DNA.
scRNA........................ small cytoplasmic RNA; any one of several
small cytoplasmic RNA molecules present
in the cytoplasm and (sometimes) nucleus
of a eukaryote.
sig_peptide.................. signal peptide coding sequence; coding
sequence for an N-terminal domain of a
secreted protein; this domain is
involved in attaching nascent
polypeptide to the membrane; leader
sequence.
snRNA........................ small nuclear RNA; any one of many small
RNA species confined to the nucleus;
several of the snRNAs are involved in
splicing or other RNA processing
reactions.
source....................... identifies the biological source of the
specified span of the sequence; this key
is mandatory; every entry will have, as
a minimum, a single source key spanning
the entire sequence; more than one
source key per sequence is permissible.
stem_loop.................... hairpin; a double-helical region formed
by base-pairing between adjacent
(inverted) complementary sequences in a
single strand of RNA or DNA.
STS.......................... Sequence Tagged Site; short, single-copy
DNA sequence that characterizes a
mapping landmark on the genome and can
be detected by PCR; a region of the
genome can be mapped by determining the
order of a series of STSs.
TATA_signal.................. TATA box; Goldberg-Hogness box; a
conserved AT-rich septamer found about
25 bp before the start point of each
eukaryotic RNA polymerase II transcript
unit which may be involved in
positioning the enzyme for correct
initiation; consensus=TATA(A or T)A(A or
T).
terminator................... sequence of DNA located either at the end
of the transcript or adjacent to a
promoter region that causes RNA
polymerase to terminate transcription;
may also be site of binding of repressor
protein.
transit_peptide.............. transit peptide coding sequence; coding
sequence for an N-terminal domain of a
nuclear-encoded organellar protein; this
domain is involved in post-translational
import of the protein into the
organelle.
tRNA......................... mature transfer RNA, a small RNA molecule
(75-85 bases long) that mediates the
translation of a nucleic acid sequence
into an amino acid sequence.
unsure....................... author is unsure of exact sequence in
this region.
V_region..................... variable region of immunoglobulin light
and heavy chains, and T-cell receptor
alpha, beta, and gamma chains; codes for
the variable amino terminal portion; can
be made up from V_segments, D_segments,
N_regions, and J_segments.
V_segment.................... variable segment of immunoglobulin light
and heavy chains, and T-cell receptor
alpha, beta, and gamma chains; codes for
most of the variable region (V_region)
and the last few amino acids of the
leader peptide.
variation.................... a related strain contains stable
mutations from the same gene (for
example, RFLPs, polymorphisms, etc.)
which differ from the presented sequence
at this location (and possibly others).
3'clip....................... 3'-most region of a precursor transcript
that is clipped off during processing.
3'UTR........................ region at the 3' end of a mature
transcript (following the stop codon)
that is not translated into a protein.
5'clip....................... 5'-most region of a precursor transcript
that is clipped off during processing.
5'UTR........................ region at the 5' end of a mature
transcript (preceding the initiation
codon) that is not translated into a
protein.
-10_signal................... pribnow box; a conserved region about 10
bp upstream of the start point of
bacterial transcription units which may
be involved in binding RNA polymerase;
consensus=TAtAaT.
-35_signal................... a conserved hexamer about 35 bp upstream
of the start point of bacterial
transcription units; consensus=TTGACa [
] or TGTTGACA [ ].
------------------------------------------------------------------------
Appendix F: List of Feature Keys Related to Protein Sequences
Source: World Intellectual Property Organization (WIPO) Handbook
on Industrial Property Information and Documentation, Standard
ST.25: Standard for the Presentation of Nucleotide and Amino Acid
Sequence Listings in Patent Applications (2009)
------------------------------------------------------------------------
Key Description
------------------------------------------------------------------------
CONFLICT.......................... different papers report differing
sequences.
VARIANT........................... authors report that sequence
variants exist.
VARSPLIC.......................... description of sequence variants
produced by alternative splicing.
[[Page 28321]]
MUTAGEN........................... site which has been experimentally
altered.
MOD_RES........................... post-translational modification of a
residue.
ACETYLATION....................... N-terminal or other.
AMIDATION......................... generally at the C-terminal of a
mature active peptide.
BLOCKED........................... undetermined N- or C-terminal
blocking group.
FORMYLATION....................... of the N-terminal methionine.
GAMMA-CARBOXYGLUTAMIC ACID of asparagine, aspartic acid,
HYDROXYLATION. proline, or lysine.
METHYLATION....................... generally of lysine or arginine.
PHOSPHORYLATION................... of serine, threonine, tyrosine,
aspartic acid or histidine.
PYRROLIDONE CARBOXYLIC ACID....... N-terminal glutamate which has
formed an internal cyclic lactam.
SULFATATION....................... generally of tyrosine.
LIPID............................. covalent binding of a lipidic
moiety.
MYRISTATE......................... myristate group attached through an
amide bond to the N-terminal
glycine residue of the mature form
of a protein or to an internal
lysine residue.
PALMITATE......................... palmitate group attached through a
thioether bond to a cysteine
residue or through an ester bond to
a serine or threonine residue.
FARNESYL.......................... farnesyl group attached through a
thioether bond to a cysteine
residue.
GERANYL-GERANYL................... geranyl-geranyl group attached
through a thioether bond to a
cysteine residue.
GPI-ANCHOR........................ glycosyl-phosphatidylinositol (GPI)
group linked to the alpha-carboxyl
group of the C-terminal residue of
the mature form of a protein.
N-ACYL DIGLYCERIDE................ N-terminal cysteine of the mature
form of a prokaryotic lipoprotein
with an amide-linked fatty acid and
a glyceryl group to which two fatty
acids are linked by ester linkages.
DISULFID.......................... disulfide bond; the `FROM' and `TO'
endpoints represent the two
residues which are linked by an
intra-chain disulfide bond; if the
`FROM' and `TO' endpoints are
identical, the disulfide bond is an
interchain one and the description
field indicates the nature of the
cross-link.
THIOLEST.......................... thiolester bond; the `FROM' and `TO'
endpoints represent the two
residues which are linked by the
thiolester bond.
THIOETH........................... thioether bond; the `FROM' and `TO'
endpoints represent the two
residues which are linked by the
thioether bond.
CARBOHYD.......................... glycosylation site; the nature of
the carbohydrate (if known) is
given in the description field.
METAL............................. binding site for a metal ion; the
description field indicates the
nature of the metal.
BINDING........................... binding site for any chemical group
(co-enzyme, prosthetic group,
etc.); the chemical nature of the
group is given in the description
field.
SIGNAL............................ extent of a signal sequence
(prepeptide).
TRANSIT........................... extent of a transit peptide
(mitochondrial, chloroplastic, or
for a microbody).
PROPEP............................ extent of a propeptide.
CHAIN............................. extent of a polypeptide chain in the
mature protein.
PEPTIDE........................... extent of a released active peptide.
DOMAIN............................ extent of a domain of interest on
the sequence; the nature of that
domain is given in the description
field.
CA_BIND........................... extent of a calcium-binding region.
DNA_BIND.......................... extent of a DNA-binding region.
NP_BIND........................... extent of a nucleotide phosphate
binding region; the nature of the
nucleotide phosphate is indicated
in the description field.
TRANSMEM.......................... extent of a transmembrane region.
ZN_FING........................... extent of a zinc finger region.
SIMILAR........................... extent of a similarity with another
protein sequence; precise
information, relative to that
sequence, is given in the
description field.
REPEAT............................ extent of an internal sequence
repetition.
HELIX............................. secondary structure: Helices, for
example, Alpha-helix, 3(10) helix,
or Pi-helix.
STRAND............................ secondary structure: Beta-strand,
for example, Hydrogen bonded beta-
strand, or Residue in an isolated
beta-bridge.
TURN.............................. secondary structure Turns, for
example, H-bonded turn (3-turn, 4-
turn, or 5-turn).
ACT_SITE.......................... amino acid(s) involved in the
activity of an enzyme.
SITE.............................. any other interesting site on the
sequence.
INIT_MET.......................... the sequence is known to start with
an initiator methionine.
NON_TER........................... the residue at an extremity of the
sequence is not the terminal
residue; if applied to position 1,
this signifies that the first
position is not the N-terminus of
the complete molecule; if applied
to the last position, it signifies
that this position is not the C-
terminus of the complete molecule;
there is no description field for
this key.
NON_CONS.......................... non consecutive residues; indicates
that two residues in a sequence are
not consecutive and that there are
a number of unsequenced residues
between them.
UNSURE............................ uncertainties in the sequence; used
to describe region(s) of a sequence
for which the authors are unsure
about the sequence assignment.
------------------------------------------------------------------------
[[Page 28322]]
Appendix G: Numeric Identifiers
----------------------------------------------------------------------------------------------------------------
Mandatory (M) or
Numeric identifier Definition Comments and format optional (O)
----------------------------------------------------------------------------------------------------------------
<110>................................ Applicant.............. If Applicant is M.
inventor, then
preferably max. of 10
names; one name per
line; preferable
format: Surname, Other
Names and/or Initials.
<120>................................ Title of Invention..... ....................... M.
<130>................................ File Reference......... Personal file reference M when filed prior to
assignment or appl.
number.
<140>................................ Current Application Specify as: US 09/ M, if available.
Number. 999,999 or PCT/US09/
99999.
<141>................................ Current Filing Date.... Specify as: yyyy-mm-dd. M, if available.
<150>................................ Prior Application Specify as: US 09/ M, if applicable
Number. 999,999 or PCT/US09/ include priority
99999. documents under 35
U.S.C. 119 and 120.
<151>................................ Prior Application Specify as: yyyy-mm-dd. M, if applicable.
Filing Date.
<160>................................ Number of SEQ ID NOs... Count includes total M.
number of SEQ ID NOs.
<170>................................ Software............... Name of software used O.
to create the
``Sequence Listing.''.
<210>................................ SEQ ID NO:#:........... Response shall be an M.
integer representing
the SEQ ID NO shown.
<211>................................ Length................. Respond with an integer M.
expressing the number
of bases or amino acid
residues.
<212>................................ Type................... Whether presented M.
sequence molecule is
DNA, RNA, or PRT
(protein). If a
nucleotide sequence
contains both DNA and
RNA fragments, the
type shall be ``DNA.''
In addition, the
combined DNA/RNA
molecule shall be
further described in
the <220> to <223>
feature section.
<213>................................ Organism............... Scientific name, i.e. M.
Genus/species, Unknown
or Artificial
Sequence. In addition,
the ``Unknown'' or
``Artificial
Sequence'' organisms
shall be further
described in the <220>
to <223> feature
section.
<220>................................ Feature................ Leave blank after M, under the following
<220>. <221-223> conditions: if ``n,''
provide for a ``Xaa,'' or a modified
description of points or unusual L-amino
of biological acid or modified base
significance in the was used in a
sequence. sequence; if ORGANISM
is ``Artificial
Sequence'' or
``Unknown''; if
molecule is combined
DNA/RNA.
<221>................................ Name/Key............... Provide appropriate M, under the following
identifier for conditions: if ``n,''
feature, from WIPO ``Xaa,'' or a modified
Standard ST.25 (2009), or unusual L-amino
Appendices E and F to acid or modified base
this subpart. was used in a
sequence.
<222>................................ Location............... Specify location within M, under the following
sequence; where conditions: if ``n,''
appropriate, state ``Xaa,'' or a modified
number of first and or unusual L-amino
last bases/amino acids acid or modified base
in feature. was used in a
sequence.
<223>................................ Other Information...... Other relevant M, under the following
information; four conditions: if ``n,''
lines maximum. ``Xaa,'' or a modified
or unusual L-amino
acid or modified base
was used in a
sequence; if ORGANISM
is ``Artificial
Sequence'' or
``Unknown''; if
molecule is combined
DNA/RNA.
<300>................................ Publication Information Leave blank after <300> O.
<301>................................ Authors................ Preferably max. of 10 O.
named authors of
publication; specify
one name per line;
preferable format:
Surname, Other Names
and/or Initials.
<302>................................ Title.................. ....................... O.
<303>................................ Journal................ ....................... O.
<304>................................ Volume................. ....................... O.
<305>................................ Issue.................. ....................... O.
<306>................................ Pages.................. ....................... O.
<307>................................ Date................... Journal date on which O.
data published;
specify as yyyy-mm-dd,
MMM-yyyy or Season-
yyyy.
<308>................................ Database Accession Accession number O.
Number. assigned by database,
including database
name.
<309>................................ Database Entry Date.... Date of entry in O.
database; specify as
yyyy-mm-dd or MMM-yyyy.
<310>................................ Patent Document Number. Document number; for O.
patent-type citations
only. Specify as, for
example, US 09/999,999.
<311>................................ Patent Filing Date..... Document filing date, O.
for patent-type
citations only;
specify as yyyy-mm-dd.
[[Page 28323]]
<312>................................ Publication Date....... Document publication O.
date, for patent-type
citations only;
specify as yyyy-mm-dd.
<313>................................ Relevant Residues...... FROM (position) TO O.
(position).
<400>................................ Sequence............... SEQ ID NO should follow M.
the numeric identifier
and should appear on
the line preceding the
actual sequence.
----------------------------------------------------------------------------------------------------------------
Andrew Hirshfeld,
Commissioner for Patents, Performing the Functions and Duties of the
Under Secretary of Commerce for Intellectual Property and Director of
the United States Patent and Trademark Office.
[FR Doc. 2021-10421 Filed 5-25-21; 8:45 am]
BILLING CODE 3510-16-P