How should variants be represented in a “Sequence Listing XML”?

Variants in a “Sequence Listing XML” should be represented according to specific guidelines. As outlined in MPEP 2413.01(g):

• A primary sequence and any variant of that sequence, each disclosed by enumeration of its residues, must be included in the sequence listing and assigned their own sequence identifier.
• A variant sequence disclosed as a single sequence with enumerated alternative residues at one or more positions should be represented by a single sequence using the most restrictive ambiguity symbol.
• Variant sequences disclosed only by reference to deletion(s), insertion(s), or substitution(s) in a primary sequence should be included in the sequence listing, potentially as annotations to the primary sequence or as separate sequences.

Proper use of feature keys and qualifiers is essential for accurately representing variants. The “replace” qualifier is used for substitutions, while the “note” qualifier can provide additional information about variations.

To learn more:

• Sequence Listing XML
• sequence variants
• feature keys
• qualifiers