jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1

Zhang, M.; Schultz, A. -K.; Calef, C.; Kuiken, C.; Leitner, T.; Korber, B.; Morgenstern, B.; Stanke, M.

doi:10.1093/nar/gkl255

jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1

Journal Article · Sat Jul 01 00:00:00 EDT 2006 · Nucleic Acids Research

DOI:https://doi.org/10.1093/nar/gkl255· OSTI ID:1625403

Zhang, M. ^[1]; Schultz, A. -K. ^[2]; Calef, C. ^[3]; Kuiken, C. ^[3]; Leitner, T. ^[3]; Korber, B. ^[4]; Morgenstern, B. ^[5]; Stanke, M. ^[2]

Abteilung Bioinformatik, Gottingen (Germany). Inst. fur Mikrobiologie und Genetik; Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; DOE/OSTI
Abteilung Bioinformatik, Gottingen (Germany). Inst. fur Mikrobiologie und Genetik
Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division
Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division; Santa Fe Inst. (SFI), Santa Fe, NM (United States)
Abteilung Bioinformatik, Gottingen (Germany). Inst. fur Mikrobiologie und Genetik; Los Alamos National Lab. (LANL), Los Alamos, NM (United States). Theoretical Division

Detecting recombinations in the genome sequence of human immunodeficiency virus (HIV-1) is crucial for epidemiological studies and for vaccine development. Herein, we present a web server for subtyping and localization of phylogenetic breakpoints in HIV-1. Our software is based on a jumping profile Hidden Markov Model (jpHMM), a probabilistic generalization of the jumping-alignment approach proposed by Spang et al. The input data for our server is a partial or complete genome sequence from HIV-1; our tool assigns regions of the input sequence to known subtypes of HIV-1 and predicts phylogenetic breakpoints. 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:: German Federal Ministry of Education and Research (BMBF); German Research Foundation (DFG); National Institutes of Health (NIH); USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division

Grant/Contract Number:: AC52-06NA25396

OSTI ID:: 1625403

Journal Information:: Nucleic Acids Research, Journal Name: Nucleic Acids Research Journal Issue: suppl_2 Vol. 34; ISSN 0305-1048

Publisher:: Oxford University PressCopyright Statement

Country of Publication:: United States

Language:: English

References (8)

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