MPEP 2418
WIPO Sequence Tool

Ninth Edition of the MPEP, Revision 07.2022, Last Revised in February 2023

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2418    WIPO Sequence Tool [R-07.2022]

[Editor Note: This section is applicable to all 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).]

To comply with rules based on WIPO Standard ST.26 (i.e., 37 CFR 1.831 - 1.835 ), patent applicants can generate a compliant "Sequence Listing XML" using WIPO Sequence, a desktop application developed by WIPO and adopted by WIPO member states, including the US. WIPO Sequence has two functions: An authoring function and a validation function. Patent applicants will be able to author and validate their "Sequence Listing XML" using WIPO Sequence to comply with the requirements of WIPO Standard ST.26. Such a "Sequence Listing XML" will be accepted by all the IPOs of the WIPO member states. Thus, the burden of generating a "Sequence Listing XML" that is acceptable across all WIPO member states will be significantly decreased for patent applicants under WIPO Standard ST.26. This tool is downloadable, free of charge, from the WIPO website. The current version of WIPO Sequence is accessible at www.wipo.int/standards/en/sequence/index.html. This version, subject to updates, will allow the public to become familiar with the tool and its dual functionalities.

WIPO Sequence will allow a user to create and save (author) patent application data and biological sequence data in a project, validate the project to ensure all required information is present, and generate a "Sequence Listing XML" in compliance with 37 CFR 1.831 - 1.834 (complying with WIPO Standard ST.26 XML format). Information can be entered into a project manually, or data can be imported from a source file in one of a number of file types. WIPO Sequence can import data from other WIPO Standard ST.26 projects, WIPO Standard ST.26 XML sequence listings, Standard ST.25 sequence listing text files, raw files, multi-sequence format files, and FASTA (FAST-All-a DNA and protein sequence alignment software package) files. Feature keys, qualifiers, and organism names are available to select from drop-down lists, simplifying the creation of sequence listings. Applicant and inventor names, as well as custom organism names, can be stored in WIPO Sequence for easy access. To facilitate the review of data entered into a project, WIPO Sequence can generate a "human-readable" version (a text version of the sequence data) of the "Sequence Listing XML."

WIPO Sequence includes an integrated validation function that will alert users to most errors in a project or "Sequence Listing XML" data. The validation function generates a report that clearly lists every detected error, the location of the error, and the detected value of the error, along with a link to the sequence in question, thereby ensuring users can correct errors before generating a final "Sequence Listing XML". While the validation function will alert a user to most errors in a project or "Sequence Listing XML", there are a small number of errors that can be detected only by human review (for example, an inappropriate organism name). In those cases, the integrated validation function will list a "warning" in the validation report, reminding users of the applicable/relevant rule and urging them to check their input values before generating a final "Sequence Listing XML".

A "Sequence Listing" in Standard ST.25 format cannot automatically be converted into WIPO Standard ST.26 format because certain data elements required for a "Sequence Listing XML" compliant with WIPO Standard ST.26 are not present in Standard ST.25. Therefore, conversion of a "Sequence Listing" in Standard ST.25 format to Standard ST.26 format necessarily requires additional input from the applicant. WIPO Sequence, supplemented by significant guidance from WIPO and the USPTO (in Annex VI and Annex VII of WIPO Standard ST.26), will help applicants accomplish this task. Users can import a Standard ST.25 "Sequence Listing" into a project, and WIPO Sequence automatically performs many of the necessary conversions. An Import Report is generated that alerts the user to all data conversions and lists all sequence entries that require additional input. In response to concerns raised regarding the USPTO’s requests for comments in 2012 and 2016, the USPTO, in conjunction with WIPO, developed Annex VII to provide detailed guidance to help applicants avoid added or deleted subject matter when converting a "Sequence Listing" from Standard ST.25 format into Standard ST.26 "Sequence Listing XML" format.

To ensure that IPOs can validate and accept sequence listing projects from applicants generated with WIPO Sequence, WIPO is developing a Standard ST.26 "Sequence Listing XML" validation tool, WIPO Sequence Validator. WIPO Sequence Validator will be for use by IPOs. WIPO Sequence Validator will be synchronized with the validation function in the WIPO Sequence tool. The USPTO is integrating WIPO Sequence Validator into its internal IT systems. The WIPO Sequence Validator will apply the same validation rules as WIPO Sequence. Therefore, filers will have a greater level of confidence that a "Sequence Listing XML" authored and validated by WIPO Sequence will comply with the USPTO rules for a "Sequence Listing XML" (37 CFR 1.831 through 1.835 ) and be accepted, given that the WIPO Sequence Validator that the USPTO will use is based on WIPO Standard ST.26.

A sample sequence listing (XML file) specimen can be found in WIPO Standard ST.26, Annex III and at www.wipo.int/standards/en/xml_material/st26/st26-annex- iii-sequence-listing-specimen.xml.