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 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/.
Zhang
Ming
M
Institut für Mikrobiologie und Genetik, Abteilung Bioinformatik, Goldschmidtstrasse 1, 37077 Göttingen, Germany.
Schultz
Anne-Kathrin
AK
Calef
Charles
C
Kuiken
Carla
C
Leitner
Thomas
T
Korber
Bette
B
Morgenstern
Burkhard
B
Stanke
Mario
M
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