How should ambiguity in sequences be represented in a sequence listing?

How should ambiguity in sequences be represented in a sequence listing?

Ambiguity in sequences should be represented using specific symbols and annotations as outlined in MPEP 2423.01 and WIPO Standard ST.25. Here’s how to handle ambiguous positions:

• For nucleotides: Use “n” to represent an unknown or ambiguous base
• For amino acids: Use “Xaa” to represent an unknown or ambiguous amino acid
• Provide additional information in the Feature section of the sequence listing

The MPEP states:

“The symbol “n” may be used to represent any nucleotide, and the symbol “Xaa” may be used to represent any amino acid. The symbol “Xaa” must be used to represent modified or unusual amino acids that cannot be represented by any other symbol.”

When using these ambiguity symbols, it’s important to provide as much additional information as possible in the Feature section to clarify the nature of the ambiguity. This might include potential alternatives for the ambiguous position or the reason for the uncertainty.

To learn more:

• sequence ambiguity
• unknown bases
• unknown amino acids
• WIPO Standard ST.25