How should sequences derived from multiple sources be represented?
Sequences derived from multiple sources or non-contiguous segments should be represented as follows: Include the constructed sequence in the “Sequence Listing XML” as a single continuous sequence. Assign the constructed sequence its own unique sequence identifier. Describe the source and construction of the sequence in the feature table using appropriate feature keys and qualifiers. 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 sequences with gaps or unknowns be represented?
Sequences with gaps or unknowns should be represented as follows: For sequences with known numbers of unknown residues: Include as one sequence in the sequence listing Use “n” for unknown nucleotides and “X” for unknown amino acids Specify the exact number of “n” or “X” residues For sequences with unknown numbers of residues between regions:…
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 sequence variants be represented in a sequence listing?
Sequence variants should be represented as follows: Each variant that meets the length threshold must be included in the sequence listing with its own sequence identifier. Variants disclosed as a single sequence with enumerated alternative residues should be represented using the most restrictive ambiguity symbol. Variants disclosed only by reference to deletions, insertions, or substitutions…
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 modified nucleotides be represented in a sequence listing?
Modified nucleotides should be represented as follows: Represent the modified nucleotide as the corresponding unmodified nucleotide (a, c, g, or t) whenever possible. If it cannot be represented by an unmodified nucleotide, use the symbol “n”. Further describe the modification in the feature table using the feature key “modified_base” and the mandatory qualifier “mod_base”. Use…
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 MoreHow should circular sequences be represented in a sequence listing?
Circular sequences should be represented as follows: For nucleotide sequences: The applicant must choose the nucleotide in residue position number 1. Numbering is continuous throughout the entire sequence in the 5′ to 3′ direction. For amino acid sequences: When an amino acid sequence is circular and the ring consists solely of amino acid residues linked…
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