How are amino acids with ambiguous positions represented in sequence listings?

How are amino acids with ambiguous positions represented in sequence listings?

The MPEP 2412.05 provides guidance on representing amino acids with ambiguous positions:

“Where an amino acid can be one of two or more alternatives at a given position in a sequence, the preferred amino acids should be shown in the sequence and the alternatives should be described in the Feature section of the Sequence Listing.”

This means that when an amino acid position can have multiple possible residues, you should:

• Include the preferred amino acid in the main sequence
• List all alternative possibilities in the Feature section of the Sequence Listing

This approach ensures that the primary sequence is clear while still providing complete information about potential variations at specific positions.

To learn more:

• ambiguous amino acids
• sequence listings
• feature section
• alternative residues