Open AccessjpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1
Author(s) -
Ming Zhang,
Anne-Kathrin Schultz,
Charles Calef,
Carla Kuiken,
Thomas Leitner,
Bette T. Korber,
Burkhard Morgenstern,
Mario Stanke
Publication year - 2006
Publication title -
nucleic acids research
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 9.008
H-Index - 537
eISSN - 1362-4954
pISSN - 0305-1048
DOI - 10.1093/nar/gkl255
Subject(s) - biology , subtyping , computational biology , genetics , web server , sequence (biology) , phylogenetic tree , genome , whole genome sequencing , gene , computer science , the internet , world wide web , programming language
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/.