PSI-BLAST pseudocounts and the minimum description length principle.

ABSTRACT: Position specific score matrices (PSSMs) are derived from multiple sequence alignments to aid in the recognition of distant protein sequence relationships. The PSI-BLAST protein database search program derives the column scores of its PSSMs with the aid of pseudocounts, added to the observed amino acid counts in a multiple alignment column. In the absence of theory, the number of pseudocounts used has been a completely empirical parameter. This article argues that the minimum description length principle can motivate the choice of this parameter. Specifically, for realistic alignments, the principle supports the practice of using a number of pseudocounts essentially independent of alignment size. However, it also implies that more highly conserved columns should use fewer pseudocounts, inc

SUBMITTER: Altschul SF 

PROVIDER: S-EPMC2647318 | biostudies-literature | 2009 Feb

REPOSITORIES: biostudies-literature