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

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W463-5. doi: 10.1093/nar/gkl255.

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/.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Genome, Viral
  • Genomics / methods*
  • HIV-1 / classification
  • HIV-1 / genetics*
  • Internet
  • Markov Chains
  • Phylogeny
  • Recombination, Genetic*
  • Software*