PSI-Search: Iterative HOE-reduced profile SSEARCH searching

28Citations
Citations of this article
56Readers
Mendeley users who have this article in their library.

This article is free to access.

Abstract

Iterative similarity searches with PSI-BLAST positionspecific score matrices (PSSMs) find many more homologs than single searches, but PSSMs can be contaminated when homologous alignments are extended into unrelated protein domains-homologous over-extension (HOE). PSI-Search combines an optimal Smith-Waterman local alignment sequence search, using SSEARCH, with the PSI-BLAST profile construction strategy. An optional sequence boundary-masking procedure, which prevents alignments from being extended after they are initially included, can reduce HOE errors in the PSSM profile. Preventing HOE improves selectivity for both PSI-BLAST and PSI-Search, but PSI-Search has ~4-fold better selectivity than PSI-BLAST and similar sensitivity at 50% and 60% family coverage. PSI-Search is also produces 2- for 4-fold fewer false-positives than JackHMMER, but is ~5% less sensitive. © The Author(s) 2012. Published by Oxford University Press.

Cite

CITATION STYLE

APA

Li, W., McWilliam, H., Goujon, M., Cowley, A., Lopez, R., & Pearson, W. R. (2012). PSI-Search: Iterative HOE-reduced profile SSEARCH searching. Bioinformatics, 28(12), 1650–1651. https://doi.org/10.1093/bioinformatics/bts240

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free