title: 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/.
authors.affiliation: Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Göttingen, Germany.
authors.forename: Ming
authors.initials: M
authors.lastname: Zhang
authors.forename: Anne-Kathrin
authors.initials: AK
authors.lastname: Schultz
authors.forename: Charles
authors.initials: C
authors.lastname: Calef
authors.forename: Carla
authors.initials: C
authors.lastname: Kuiken
authors.forename: Thomas
authors.initials: T
authors.lastname: Leitner
authors.forename: Bette
authors.initials: B
authors.lastname: Korber
authors.forename: Burkhard
authors.initials: B
authors.lastname: Morgenstern
authors.forename: Mario
authors.initials: M
authors.lastname: Stanke
mesh_terms: D016679:Genome, Viral; D023281:Genomics / Q000379:methods*; D015497:HIV-1 / Q000145:classification / Q000235:genetics*; D020407:Internet; D008390:Markov Chains; D010802:Phylogeny; D011995:Recombination, Genetic; D012984:Software