title: Retrieval accuracy, statistical significance and compositional similarity in protein sequence database searches.
abstract: 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.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, NIH, DHHS, Bethesda, MD 20894, USA.
authors.forename: Yi-Kuo
authors.initials: YK
authors.lastname: Yu
authors.forename: E Michael
authors.initials: EM
authors.lastname: Gertz
authors.forename: Richa
authors.initials: R
authors.lastname: Agarwala
authors.forename: Alejandro A
authors.initials: AA
authors.lastname: Schäffer
authors.forename: Stephen F
authors.initials: SF
authors.lastname: Altschul
mesh_terms: D003627:Data Interpretation, Statistical; D030562:Databases, Protein; D015203:Reproducibility of Results; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein; D012984:Software