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

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...

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Detalles Bibliográficos
Autores principales: Zhang, Ming, Schultz, Anne-Kathrin, Calef, Charles, Kuiken, Carla, Leitner, Thomas, Korber, Bette, Morgenstern, Burkhard, Stanke, Mario
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2006
Materias:
Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538796/
https://www.ncbi.nlm.nih.gov/pubmed/16845050
http://dx.doi.org/10.1093/nar/gkl255
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author Zhang, Ming
Schultz, Anne-Kathrin
Calef, Charles
Kuiken, Carla
Leitner, Thomas
Korber, Bette
Morgenstern, Burkhard
Stanke, Mario
author_facet Zhang, Ming
Schultz, Anne-Kathrin
Calef, Charles
Kuiken, Carla
Leitner, Thomas
Korber, Bette
Morgenstern, Burkhard
Stanke, Mario
author_sort Zhang, Ming
collection PubMed
description 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 .
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spelling pubmed-15387962006-08-18 jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1 Zhang, Ming Schultz, Anne-Kathrin Calef, Charles Kuiken, Carla Leitner, Thomas Korber, Bette Morgenstern, Burkhard Stanke, Mario Nucleic Acids Res Article 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 . Oxford University Press 2006-07-01 2006-07-14 /pmc/articles/PMC1538796/ /pubmed/16845050 http://dx.doi.org/10.1093/nar/gkl255 Text en © 2006 The Author(s)
spellingShingle Article
Zhang, Ming
Schultz, Anne-Kathrin
Calef, Charles
Kuiken, Carla
Leitner, Thomas
Korber, Bette
Morgenstern, Burkhard
Stanke, Mario
jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
title jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
title_full jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
title_fullStr jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
title_full_unstemmed jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
title_short jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
title_sort jphmm at gobics: a web server to detect genomic recombinations in hiv-1
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1538796/
https://www.ncbi.nlm.nih.gov/pubmed/16845050
http://dx.doi.org/10.1093/nar/gkl255
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