scoring, include reverse

Syntax

The value for this parameter can be yes, no or only.

Notes

1. The default value for this parameter is no.

Description

Due to the structure of some older search engines, no statistical information is compiled about the validity of the results. As an after-the-fact kluge to correct this problem, it has become common practice to repeat a search using the same set of protein sequences, with the protein sequences altered to be written in reverse order (a so-called "decoy search"). By comparing the scores produced by this "decoy" search and the normal search, it is possible to very crudely estimate whether a result is potentially a false positive.

The statistical analysis done by X! Tandem makes this type of crude estimate unnecessary. However, to make comparisons possible, X! Tandem has a protein sequence reverse method built in. When the value of this parameter is yes, the protein sequences are first searched normally and then reversed in memory and searched again. The tag ":reversed" is added to the protein description, so that peptides corresponding to reversed sequences can be distinguished in the output. Using this feature regularly is not recommended, as it doubles the time required to perform a search and the use of reversed searches for validation has no general statistical value.

When the value is only, then results for the normal sequences will not be tested: only the reversed sequences will be used.