title: jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus.
abstract: jpHMM is a very accurate and widely used tool for recombination detection in genomic sequences of HIV-1. Here, we present an extension of jpHMM to analyze recombinations in viruses with circular genomes such as the hepatitis B virus (HBV). Sequence analysis of circular genomes is usually performed on linearized sequences using linear models. Since linear models are unable to model dependencies between nucleotides at the 5'- and 3'-end of a sequence, this can result in inaccurate predictions of recombination breakpoints and thus in incorrect classification of viruses with circular genomes. The proposed circular jpHMM takes into account the circularity of the genome and is not biased against recombination breakpoints close to the 5'- or 3'-end of the linearized version of the circular genome. It can be applied automatically to any query sequence without assuming a specific origin for the sequence coordinates. We apply the method to genomic sequences of HBV and visualize its output in a circular form. jpHMM is available online at http://jphmm.gobics.de for download and as a web server for HIV-1 and HBV sequences.
authors.affiliation: Abteilung für Bioinformatik, Institut für Mikrobiologie und Genetik, Georg-August-Universität Göttingen, Goldschmidtstr. 1, 37077 Göttingen, Germany. anne@gobics.de
authors.forename: Anne-Kathrin
authors.initials: AK
authors.lastname: Schultz
authors.forename: Ingo
authors.initials: I
authors.lastname: Bulla
authors.forename: Mariama
authors.initials: M
authors.lastname: Abdou-Chekaraou
authors.forename: Emmanuel
authors.initials: E
authors.lastname: Gordien
authors.forename: Burkhard
authors.initials: B
authors.lastname: Morgenstern
authors.forename: Fabien
authors.initials: F
authors.lastname: Zoaulim
authors.forename: Paul
authors.initials: P
authors.lastname: Dény
authors.forename: Mario
authors.initials: M
authors.lastname: Stanke
mesh_terms: D016679:Genome, Viral; D023281:Genomics / Q000379:methods; D006515:Hepatitis B virus / Q000235:genetics*; D020407:Internet; D008390:Markov Chains; D011995:Recombination, Genetic; D016415:Sequence Alignment; D012984:Software