What is the required file format for a “Sequence Listing XML” submission?
The “Sequence Listing XML” must be in XML format, as specified in MPEP 2413.02. The MPEP states: “Be in XML format, where all permitted printable characters (including the space character) and nonprintable (control) characters are defined in paragraph 40 of WIPO Standard ST.26 (incorporated by reference, see § 1.839).“ This means that the file must…
Read MoreWhat is a “Sequence Listing XML” and why must it be valid according to the DTD?
A “Sequence Listing XML” is a standardized format for presenting nucleotide and/or amino acid sequences in patent applications. It must be valid according to the Document Type Definition (DTD) as specified in MPEP § 2413.01(b) and 37 CFR 1.833(b)(1). The MPEP states: “The ‘Sequence Listing XML’ presented in accordance with paragraph (a) of this section…
Read MoreCan I submit both a “Sequence Listing XML” and a “Sequence Listing” in the same application?
No, for applications filed on or after July 1, 2022, you cannot submit both a “Sequence Listing XML” and a “Sequence Listing” in the same application. The USPTO has specific rules regarding this matter. According to MPEP 2413.03: “For applications filed on or after July 1, 2022, the USPTO patent electronic filing system will prohibit…
Read MoreWhat are the requirements for submitting a sequence listing as part of a patent application?
When submitting a sequence listing as part of a patent application, there are specific requirements that must be met: The sequence listing must be submitted as a separate part of the disclosure. It should be presented on its own page or as a separate text file. The sequence listing must comply with the requirements of…
Read MoreWhat is considered a “sequence” for the purpose of assigning sequence identifiers?
According to MPEP 2412.05(a), a “sequence” that requires a separate sequence identifier is defined by WIPO Standard ST.26, paragraph 7, as: An unbranched sequence or a linear region of a branched sequence containing ten or more specifically defined nucleotides, with adjacent nucleotides joined by a 3′ to 5′ (or 5′ to 3′) phosphodiester linkage or…
Read MoreWhere can I find a sample Sequence Listing XML file?
A sample Sequence Listing XML file is available for reference. According to MPEP 2418: 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. This sample file can be useful for understanding the structure and content of a compliant Sequence Listing XML file under WIPO Standard…
Read MoreHow are residues represented in sequence enumerations according to WIPO Standard ST.26?
WIPO Standard ST.26 specifies two ways to represent residues in sequence enumerations: Individual representation: Each residue is represented by a name, abbreviation, symbol, or structure. For example, “HHHHHHQ” or “HisHisHisHisHisHisGln”. Shorthand formula: Multiple residues are represented by a condensed notation. For example, “His6Gln”. As stated in MPEP 2412.02(a): “WIPO Standard ST.26 specifies that ‘enumeration of…
Read MoreHow are unknown nucleotides represented in a patent application?
According to MPEP 2412.05(b), unknown nucleotides in patent applications should be represented as follows: Use the symbol “n” to represent any unknown nucleotide in the sequence Further describe the unknown nucleotide in a feature table using the feature key “unsure” The symbol “n” is equivalent to only one residue The MPEP states, “Any “unknown” nucleotide…
Read MoreHow should intentionally skipped sequences be represented in the “Sequence Listing XML”?
According to MPEP 2412.05(a), intentionally skipped sequences must be included in the “Sequence Listing XML” and represented as follows: Use the element SequenceData and its attribute sequenceIDNumber, providing the sequence identifier of the skipped sequence as the value. Include the elements INSDSeq_length, INSDSeq_moltype, and INSDSeq_division, but with no value provided. Do not include the element…
Read MoreHow should sequences with defined regions separated by undisclosed gaps be represented in a Sequence Listing XML?
The MPEP 2412.05(e) provides specific guidance on how to represent sequences with defined regions separated by undisclosed gaps in a Sequence Listing XML: “A nucleotide and/or amino acid sequence that contains regions of specifically defined residues separated by one or more gaps of an unknown or undisclosed number of residues must be listed in the…
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