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.
CITATION STYLE
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
Mendeley helps you to discover research relevant for your work.