ArticleBioinformatics (Oxford, England)2009
HHsvm: fast and accurate classification of profile-profile matches identified by HHsearch.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Cyclic Tetra-Adenylate (cABiomolecules · 2021Article
- An ancient evolutionary connection between Ribonuclease A and EndoU families.RNA (New York, N.Y.) · 2020Article
- Identification of divergent protein domains by combining HMM-HMM comparisons and co-occurrence detection.PloS one · 2014Article
- Structural studies of E73 from a hyperthermophilic archaeal virus identify the "RH3" domain, an elaborated ribbon-helix-helix motif involved in DNA recognition.Biochemistry · 2012Article
- Proteomic analysis of Sulfolobus solfataricus during Sulfolobus Turreted Icosahedral Virus infection.Journal of proteome research · 2012Article
- Identification of new homologs of PD-(D/E)XK nucleases by support vector machines trained on data derived from profile-profile alignments.Nucleic acids research · 2011Article
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Abstract
motivationRecently developed profile-profile methods rival structural comparisons in their ability to detect homology between distantly related proteins. Despite this tremendous progress, many genuine relationships between protein families cannot be recognized as comparisons of their profiles result in scores that are statistically insignificant.
resultsUsing known evolutionary relationships among protein superfamilies in SCOP database, support vector machines were trained on four sets of discriminatory features derived from the output of HHsearch. Upon validation, it was shown that the automatic classification of all profile-profile matches was superior to fixed threshold-based annotation in terms of sensitivity and specificity. The effectiveness of this approach was demonstrated by annotating several domains of unknown function from the Pfam database. AVAILABILITY: Programs and scripts implementing the methods described in this manuscript are freely available from http://hhsvm.dlakiclab.org/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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