jpHMM: Improving the reliability of recombination prediction in HIV-1

Schultz, Anne-Kathrin; Zhang, Ming; Bulla, Ingo; Leitner, Thomas; Korber, Bette; Morgenstern, Burkhard; Stanke, Mario

doi:10.1093/nar/gkp371

jpHMM: Improving the reliability of recombination prediction in HIV-1

Journal Article · Thu May 14 00:00:00 EDT 2009 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkp371· OSTI ID:1625462

Schultz, Anne-Kathrin ^[1]; Zhang, Ming ^[2]; Bulla, Ingo ^[3]; Leitner, Thomas ^[4]; Korber, Bette ^[5]; Morgenstern, Burkhard ^[3]; Stanke, Mario ^[3]

Georg-August-Universitat Gottingen (Germany). Abteilung fur Bioinformatik. Institut fur Mikrobiologie und Genetik; DOE/OSTI
Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Center for Nonlinear Studies
Georg-August-Universitat Gottingen (Germany). Abteilung fur Bioinformatik. Institut fur Mikrobiologie und Genetik
Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Santa Fe Inst. (SFI), Santa Fe, NM (United States)

Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and assigns to each position of the sequence one of the major HIV-1 subtypes. Since incorrect subtype assignment or recombination prediction may lead to wrong conclusions in epidemiological or vaccine research, information about the reliability of the predicted parental subtypes and breakpoint positions is valuable. For this reason, we extended the output of jpHMM to include such information in terms of ‘uncertainty’ regions in the recombination prediction and an interval estimate of the breakpoint. Both types of information are computed based on the posterior probabilities of the subtypes at each query sequence position. Our results show that this extension strongly improves the reliability of the jpHMM recombination prediction. The jpHMM is available online at http:// jphmm.gobics.de/.

View Accepted Manuscript (DOE)

Research Organization:: Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1625462

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: Web Server Vol. 37; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

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