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

ABSTRACT: 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/.

SUBMITTER: Zhang M

PROVIDER: S-EPMC1538796 | biostudies-literature | 2006 Jul

REPOSITORIES: biostudies-literature

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

Zhang Ming M Schultz Anne-Kathrin AK Calef Charles C Kuiken Carla C Leitner Thomas T Korber Bette B Morgenstern Burkhard B Stanke Mario M

Nucleic acids research 20060701 Web Server issue

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 ...[more]

PMID: 16845050

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