How 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…
Read MoreHow are sequences with known numbers of ‘n’ or ‘X’ residues between defined regions represented in a Sequence Listing XML?
According to MPEP 2412.05(e), sequences with known numbers of ‘n’ or ‘X’ residues between defined regions are represented as a single sequence in the Sequence Listing XML. The MPEP states: “A nucleotide and/or amino acid sequence that contains regions of specifically defined residues separated by one or more regions of contiguous ‘n’ or ‘X’ residues,…
Read MoreHow should sequence variants be represented in a Sequence Listing XML?
Representation of sequence variants in a Sequence Listing XML is important for accurately describing genetic variations. According to MPEP 2413.01(g): Each primary sequence and its variants must be included in the sequence listing with their own sequence identifiers. Variants disclosed as a single sequence with enumerated alternative residues should be represented by a single sequence…
Read MoreHow should a sequence constructed from non-contiguous segments be represented in a Sequence Listing XML?
According to MPEP 2412.05(e), a sequence constructed as a single continuous sequence from non-contiguous segments must be listed in the Sequence Listing XML as a single sequence with its own identifier. Specifically, the MPEP states: “A nucleotide and/or amino acid sequence that is constructed as a single continuous sequence derived from one or more non-contiguous…
Read MoreHow should modified residues be represented in a Sequence Listing XML?
Representing modified residues correctly in a Sequence Listing XML is crucial for accurately describing non-standard amino acids or nucleotides. According to MPEP 2413.01(g): “For the ‘note’ qualifier, where the variant residue is a modified residue not set forth in Table 2, the complete unabbreviated name of the modified residue must be provided as the qualifier…
Read MoreHow should coding sequences (CDS) be represented in a Sequence Listing XML?
Coding sequences (CDS) in a Sequence Listing XML should be represented using the “CDS” feature key. According to MPEP 2413.01(g): “The ‘CDS’ feature key may be used to identify coding sequences, i.e., sequences of nucleotides which correspond to the sequence of amino acids in a protein and the stop codon. The location of the ‘CDS’…
Read MoreWhat is required when submitting a replacement “Sequence Listing XML” under 37 CFR 1.835(b)?
When submitting a replacement “Sequence Listing XML” under 37 CFR 1.835(b), the following items are required: A compliant replacement “Sequence Listing XML” file An amendment to the specification incorporating the new file by reference A statement identifying the location of all changes A statement identifying the basis for all changes A statement that no new…
Read MoreWhat is the proper format for incorporating the Sequence Listing XML by reference?
What is the proper format for incorporating the Sequence Listing XML by reference? The proper format for incorporating the Sequence Listing XML by reference is crucial for compliance with USPTO requirements. According to MPEP 2413.04, the incorporation by reference statement should follow a specific format: “The incorporation by reference statement must include the name of…
Read MoreHow should language-dependent free text be presented in a Sequence Listing XML?
Language-dependent free text in a Sequence Listing XML should be presented as follows: In English within the INSDQualifier_value element In a language other than English within the NonEnglishQualifier_value element Or in both elements The MPEP states: “Language-dependent free text must be presented in the INSDQualifier_value element in English, or in the NonEnglishQualifier_value element in a…
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