output, one sequence copy

Syntax

The value for this parameter can be yes or no.

Notes

1. If this parameter is invalid or absent, the default value no will be used.

Description

Protein sequences are normally stored in the X! Tandem output file format, represented in BIOML. If multiple peptides from a single protein sequence are found, then that protein sequence is by default reported for each peptide. If this parameter is set to yes, then the full protein sequence is only recorded for the first peptide in a file corresponding to that protein. Subsequent peptides only have the protein's unique identifier (UID) recorded. This UID is assigned by X! Tandem, based on the ordinal position of the protein in a sequence file. For example, if a protein was the 123rd protein read from a file during a search, then that protein's UID would be "123".