Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches - Protein

Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches
October 26, 2006
Yi-Kuo Yu, E. Michael Gertz, Richa Agarwala, Alejandro A. Sch?ffer and Stephen F. Altschul
Nucleic Acids Research
Protein sequence database search programs may be evaluated both for their retrieval accuracy?the ability to separate meaningful from chance similarities?and for the accuracy of their statistical assessments of reported alignments. However, methods for improving statistical accuracy can degrade retrieval accuracy by discarding compositional evidence of sequence relatedness. This evidence may be preserved by combining essentially independent measures of alignment and compositional similarity into a unified measure of sequence similarity. A version of the BLAST protein database search program, modified to employ this new measure, outperforms the baseline program in both retrieval and statistical accuracy on ASTRAL, a SCOP-based test set.
Please visit the web site to view the article in its entirety.