How should unknown amino acids be represented in sequence listings?
How should unknown amino acids be represented in sequence listings? The MPEP 2412.05 provides specific guidance on representing unknown amino acids in sequence listings: “The symbol “Xaa” must be used to represent an unknown or other amino acid.” This means that whenever an amino acid in a sequence is unknown or cannot be confidently identified,…
Read MoreWhat symbols are used for termination codons in nucleotide sequences?
What symbols are used for termination codons in nucleotide sequences? According to MPEP 2412.05, termination codons in nucleotide sequences are represented by specific symbols: “The symbols “TAA,” “TGA,” or “TAG” should be used to represent termination codons.” This means that when including a termination codon in a nucleotide sequence listing, you should use one of…
Read MoreHow 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 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?
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 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 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…
Read MoreWhat format should be used for nucleotide sequences in patent applications?
What format should be used for nucleotide sequences in patent applications? According to MPEP 2412.05, nucleotide sequences in patent applications must follow a specific format: “A nucleotide sequence must be presented as a lowercase sequence using the standard symbols for nucleotides.” This means that when presenting nucleotide sequences in your patent application: Use lowercase letters…
Read MoreWhat symbols should be used to represent nucleotide sequences?
According to WIPO Standard ST.26, paragraph 13, all nucleotides in a sequence must be represented using the symbols in Table 1: List of Nucleotides Symbols. Only lowercase letters must be used. The most important symbols are: a – for adenine c – for cytosine g – for guanine t – for thymine in DNA or…
Read MoreWhat are the accepted symbols for modified nucleotides in sequence listings?
What are the accepted symbols for modified nucleotides in sequence listings? According to MPEP 2412.05, modified nucleotides can be represented in sequence listings using specific symbols. The MPEP states: “Modified nucleotides may be represented in the sequences as described in paragraph 3 of this section with the symbol “n,” and must be further described in…
Read More