2422.03(a) “Sequence Listing” Submitted as ASCII Plain Text Files [R-07.2022]

2422.03(a) “Sequence Listing” Submitted as ASCII Plain Text Files [R-07.2022]

[Editor Note: This section is not applicable to applications filed on or after July 1, 2022, having disclosures of nucleotide and/or amino acid sequences as defined in 37 CFR 1.831(b). See MPEP §§ 2412–2419 for guidance on WIPO ST.26 requirements for applications filed on or after July 1, 2022.]

The Legal Framework for Patent Electronic System (www.uspto.gov/sites/default/files/ documents/2019LegalFrameworkPES.pdf) and MPEP § 502.05 provide detailed information pertaining to filing applications and other documents via the USPTO patent electronic filing system. The information below is specific to “Sequence Listing” submissions via the USPTO patent electronic filing system.

Pursuant to the Legal Framework for Patent Electronic System, applicants may submit a “Sequence Listing” under 37 CFR 1.821 as an ASCII plain text file via the USPTO patent electronic filing system or on read-only optical disc(s), provided the specification contains a statement in a separate paragraph (preferably on the first page) that incorporates by reference the material in the ASCII plain text file identifying the name of the ASCII plain text file, the date of creation, and the size of the ASCII plain text file in bytes. See 37 CFR 1.77(b)(5) and 1.823(b)(1). An exception is that an incorporation by reference statement is not required in an international application and is not required in an application file under 35 U.S.C. 371 where the “Sequence Listing” has been previously communicated to the International Bureau or originally filed in the USPTO and complies with Patent Cooperation Treaty Rule 5.2. See 37 CFR 1.821(c), 1.823(b)(2), and 1.825(c). The requirements of 37 CFR 1.52(e) for documents submitted on read-only optical disc(s) are not applicable to a “Sequence Listing” submitted as ASCII plain text files via the USPTO patent electronic filing system. However, each text file must be an ASCII plain text file and have a file name with a “.txt” extension. See 37 CFR 1.824.

I. ASCII PLAIN TEXT FILES SERVE AS BOTH THE “SEQUENCE LISTING” AND THE CRF

It is recommended that a “Sequence Listing” be submitted as an ASCII plain text file via the USPTO patent electronic filing system rather than as a PDF image file. See subsection IV, below, for information regarding filing an international application (PCT) with a sequence listing ASCII plain text file via the USPTO patent electronic filing system.

If the “Sequence Listing” is submitted in an application filed under 35 U.S.C. 111(a) as an ASCII plain text file in compliance with 37 CFR 1.824 via the USPTO patent electronic filing system and applicant has not filed a “Sequence Listing” as a PDF image file or on physical sheets of paper, the ASCII plain text file will serve as both the “Sequence Listing” under 37 CFR 1.821(c) and the CRF of the “Sequence Listing” under 37 CFR 1.821(e). See 37 CFR 1.821(e)(1). Similarly, if the “Sequence Listing” is filed in a national stage application submitted under 35 U.S.C. 371 as an ASCII plain text file in compliance with 37 CFR 1.824 via the USPTO patent electronic filing system, the ASCII plain text file will serve as both the “Sequence Listing” under 37 CFR 1.821(c) and the CRF of the “Sequence Listing” under 37 CFR 1.821(e). Thus, the following are not required and should not be submitted: (1) a second copy of the “Sequence Listing” as a PDF image file or on physical sheets of paper; and (2) a statement under 37 CFR 1.821(e)(1)(ii) or (2)(ii) (indicating that the sequence information contained in the “Sequence Listing” under 37 CFR 1.821(c) and CRF copy of the “Sequence Listing” under 37 CFR 1.821(e)(1)(ii) or (2)(ii) are identical). Also, the practice of CRF transfers has been eliminated. Checker software that may be used to check a “Sequence Listing” for compliance with the requirements of 37 CFR 1.824 is available on the USPTO website at www.uspto.gov/patents-getting-started/patent-basics/ types-patent-applications/utility-patent/checker-version-446. The User Notes on the Checker website should be consulted for an explanation of the scope of errors and content that is able to be verified by the Checker software.

If a user adds a “Sequence Listing” (under PCT Rule 13ter) as an ASCII plain text file via the USPTO patent electronic filing system in response to a requirement under 37 CFR 1.821(h), the “Sequence Listing” ASCII plain text file must be accompanied by a statement that the ASCII plain text file does not go beyond the disclosure in the international application as filed and the late furnishing fee as set forth in 37 CFR 1.445(a)(5). However, if a user submits an amendment to add or replace a “Sequence Listing” (under 37 CFR 1.821(c)) as an ASCII plain text file via the USPTO electronic filing system in response to a requirement under 37 CFR 1.821(g), the submission must comply with 37 CFR 1.825. See MPEP § 2426.

In applications filed under 35 U.S.C. 111(a) and 371, submission of the “Sequence Listing” as a PDF image file or on physical sheets of paper is not recommended. Where the “Sequence Listing” is submitted as a PDF image or on physical sheets of paper, applicant must provide the CRF required by 37 CFR 1.821(e)(1)(i). Note that the “Sequence Listing” in the PDF image file or on physical sheets of paper will not be excluded when determining the application size fee. The USPTO prefers the submission of sequence information in an ASCII plain text file via the USPTO electronic filing system because as stated above, if in an application filed under 35 U.S.C. 111(a) or 35 U.S.C. 371 applicant has not filed a second copy of the “Sequence Listing” as a PDF image file or on physical sheets of paper (see 37 CFR 1.821(e)(1)), the ASCII plain text file will serve as both the “Sequence Listing” required by 37 CFR 1.821(c) and the CRF required by 37 CFR 1.821(e).

II. APPLICATION SIZE FEE

Any “Sequence Listing” or CRF of a “Sequence Listing” submitted as an ASCII plain text file via the USPTO patent electronic filing system that is in compliance with 37 CFR 1.821(c) or (e) will be excluded when determining the application size fee required by 37 CFR 1.16(s) or 1.492(j) as per 37 CFR 1.52(f)(2). A “Sequence Listing” submitted as a PDF image file via the USPTO patent electronic filing system or on read-only optical disc will not be excluded when determining the application size fee.

See subsection IV, below, for additional information regarding application size fees in an international application (PCT).

III. SIZE RESTRICTIONS FOR ASCII PLAIN TEXT FILES

One hundred (100) megabytes is the size limit for “Sequence Listing” ASCII plain text files submitted via the USPTO patent electronic filing system, and compression is not allowed for a “Sequence Listing” submitted via the USPTO patent electronic filing system. If a user wishes to submit a “Sequence Listing” ASCII plain text file that exceeds 100 megabytes, it is recommended that the user file the application without the “Sequence Listing” using the USPTO patent electronic filing system to obtain the application number and confirmation number, and then file the “Sequence Listing” on read-only optical disc(s) in accordance with 37 CFR 1.52(e) and 1.824 on the same day by using Priority Mail Express® from the USPS in accordance with 37 CFR 1.10, or hand delivery, in order to secure the same filing date for all parts of the application. Note: a submission of a “Sequence Listing” in electronic form of 300 MB or more in size is subject to an oversized submission fee set forth in 37 CFR 1.21(o). See 37 CFR 1.52(f)(3). Alternatively, a user may submit the application on physical sheets of paper and include the “Sequence Listing” ASCII plain text file on read-only optical disc(s) in accordance with 37 CFR 1.52(e). “Sequence Listing” ASCII plain text files may not be divided into multiple files so as to not exceed the 100 MB size limit for filing via the USPTO patent electronic filing system, and any “Sequence Listing” greater than 100 MB must be submitted on read-only optical disc(s). If the “Sequence Listing” is filed on a read-only optical disc, the ”Sequence Listing” must be a single file, and any not compressed file must be contained on a single read-only optical disc. However, a compressed 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 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. See 37 CFR 1.52(e)(5) and 1.824(b).

See subsection IV.B, below, for information regarding submission of a sequence listing text file that exceeds 100 megabytes in an international application (PCT) filed via the USPTO patent electronic filing system.

The current size limit on the USPTO patent electronic filing system for ASCII plain text file submissions of “Large Tables” and a “Computer Program Listing Appendix” is 25 megabytes per submission, and compression is not allowed for “Large Tables” and a “Computer Program Listing Appendix” submitted as ASCII plain text files via the USPTO patent electronic filing system. Files above the 25 MB limit for “Large Tables” and a “Computer Program Listing Appendix” may be either (1) broken up into multiple files that are no larger than 25 MB each and those smaller files may be submitted via the USPTO patent electronic filing system or (2) submitted on read-only optical disc(s) (see 37 CFR 1.52(e)). If the user chooses to break up a “Large Table” or “Computer Program Listing Appendix” file so that it may be submitted via the USPTO patent electronic filing system, the file names must indicate their order (e.g., “1 of X”, “2 of X”). If a user wishes to file an application with a “Large Table” or “Computer Program Listing Appendix” ASCII plain text file that is larger than 25 megabytes, it is recommended that the user file the application without the “Large Table” or “Computer Program Listing Appendix” using the USPTO patent electronic filing system to obtain the application number and confirmation number, and then file the “Large Table” or “Computer Program Listing Appendix” on read-only optical disc(s) in accordance with 37 CFR 1.52(e) and 1.58(c) or 1.96(c) on the same day by using Priority Mail Express® from the USPS in accordance with 37 CFR 1.10, or hand delivery, in order to secure the same filing date for all parts of the application. Alternatively, a user may submit the application on physical sheets of paper and include the “Large Table” or “Computer Program Listing Appendix” ASCII plain text file on read-only optical disc(s) in accordance with 37 CFR 1.52(e) in order to secure the same filing date for all parts of the application. See 37 CFR 1.58(f) and 37 CFR 1.96(c)(4).

IV. FILING A SEQUENCE LISTING IN INTERNATIONAL APPLICATIONS (PCT) VIA THE USPTO PATENT ELECTRONIC FILING SYSTEM

A.Sequence Listing Must Be Presented as a Separate Part of the Description

Under PCT Rule 5.2(a), “where the international application contains disclosure of one or more nucleotide and/or amino acid sequences, the description shall contain a sequence listing complying with the standard provided for in the Administrative Instructions and presented as a separate part of the description in accordance with that standard”. The standard is set forth in the PCT Administrative Instructions Annex C, entitled Standard for the Presentation of Nucleotide and Amino Acid Sequence Listings in International Patent Applications Under the PCT. When filing an international application (PCT) using the USPTO patent electronic filing system, it is highly recommended to submit a sequence listing as a single ASCII plain text file with a “.txt” extension on the international filing date. Note that 100 megabytes is the size limit for submitting a sequence listing ASCII plain text file via the USPTO patent electronic filing system. See subsection IV.B, below. Although it is not recommended, applicant can also submit the sequence listing in a PCT application as a PDF image file as part of the application on the international filing date.

If the sequence listing is submitted as an ASCII plain text file when filing a new international application (PCT), applicant need not and should not submit any additional copies, including PDF image files. The single ASCII plain text file is preferred because the ASCII plain text file will serve both as the sequence listing part of the description required under PCT Rule 5.2 and the electronic form under PCT Rule 13ter.1(a) in the absence of a PDF sequence listing file. The check list (Box No. IX) of the PCT Request (form PCT/RO/101) provided via the USPTO patent electronic filing system together with the international application (PCT) must indicate that the sequence listing submitted as an ASCII plain text file forms part of the international application. Furthermore, the statement as set forth in paragraph 4(v) of the AI Annex C (Administrative Instructions under the PCT, Annex C), that “the information recorded in electronic form furnished under PCT Rule 13ter is identical to the sequence listing as contained in the international application,” is not necessary.

Submission of the sequence listing part of the description as a PDF image file in a new international application (PCT) is not recommended because, where the application does not contain a sequence listing as an ASCII plain text file, the International Searching Authority or the International Preliminary Authority may invite applicant to furnish a copy of the sequence listing in ASCII plain text format for the purposes of international search and/or preliminary examination. Any sequence listing submitted in response to this invitation will not form part of the application.

When a sequence listing is filed via the USPTO patent electronic filing system in a new PCT international application as both a PDF image file and an ASCII plain text file, but the Request form Box No. IX does not indicate which one forms part of the international application, the PDF image copy of the sequence listing will be considered to form part of the application and the ASCII plain text file will be considered to be an accompanying item for search purposes under PCT Rule 13ter.1(a) only.

The international filing fee for an international application (PCT) that includes a sequence listing, filed via the USPTO patent electronic filing system, is calculated based on the type of sequence listing file that is part of the description of the international application (PCT). A sequence listing filed as an ASCII plain text file will not be included in the sheet count of the international application (PCT). A sequence listing filed as a PDF image file will be included in the sheet count of the international application (PCT), when it is part of the description. When a new PCT international application is filed via the USPTO patent electronic filing system and contains the sequence listing part of the description as a PDF image file and a sequence listing ASCII plain text to be used only for search purposes under PCT Rule 13ter.1(a), the sheets of the PDF image file will count towards excess sheet fees, if any.

B.File Size and Quantity Limits

One hundred (100) megabytes is the size limit for sequence listing ASCII plain text files submitted via the USPTO patent electronic filing system. See 37 CFR 1.824(b)(1). Sequence listing ASCII plain text files must not be partitioned into multiple files for filing via the USPTO patent electronic filing system. The sequence listing must be in a single ASCII plain text file.

Applicant may use the USPTO patent electronic filing system to file part of the international application (PCT) and to obtain the international application (PCT) number and the confirmation number, and then file the remainder of the international application (PCT) on the same day as one or more follow-on submissions using the USPTO patent electronic filing system, in order to secure the same filing date for all parts of the international application (PCT). However, applicant is not permitted to file part of the international application (PCT) electronically via the USPTO patent electronic filing system, and then file the remainder of the international application (PCT) on paper to secure a filing date of all parts of the international application (PCT).

In the situation where applicant needs to file a sequence listing that is over one hundred (100) megabytes, applicant may use the USPTO patent electronic filing system to file the international application (PCT) without the sequence listing to obtain the international application (PCT) number and the confirmation number, and then file the sequence listing on read-only optical discs on the same day by using Priority Mail Express® from the USPS in accordance with 37 CFR 1.10, or by hand delivery, in order to secure the same filing date for all parts of the international application (PCT). However, the read-only optical discs must not contain PDF image files and must fully comply with the guidelines for filing a sequence listing on electronic media. The check list of the PCT Request provided via the USPTO patent electronic filing system together with the international application (PCT) must indicate that the sequence listing will be filed separately on physical data carrier(s), on the same day and in the form of an Annex C/ST.25 text file. The sequence listing must be a single file, but the file may be split for submission on multiple physical media using software designed to divide a file into multiple files for subsequent concatenation. If the user breaks up a sequence listing for submission on multiple read-only optical discs, the read-only optical discs must be labeled to indicate their order (e.g., “1 of X”, “2 of X”).

Submissions of very lengthy sequence listings (300 MB or over a.k.a. mega-sequence listings) in international applications are not subject to the mega-sequence listing submission fees set forth in 37 CFR 1.21(o). However, for mega-sequence listing submissions on or after January 16, 2018, the fee under 37 CFR 1.21(o) does apply to the submission of mega-sequence listings received in national stage applications under 35 U.S.C. 371, including mega-sequence listings received by the Office pursuant to PCT Article 20. Similarly, if an international application is filed at RO/US with a mega-sequence listing, and thereafter a bypass continuing application is filed under 35 U.S.C. 111(a), the fee under 37 CFR 1.21(o) will be due in the continuing application for mega-sequence listing submissions on or after January 16, 2018. See 37 CFR 1.52(f)(3).