title: jpHMM: improving the reliability of recombination prediction in HIV-1.
abstract: Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and assigns to each position of the sequence one of the major HIV-1 subtypes. Since incorrect subtype assignment or recombination prediction may lead to wrong conclusions in epidemiological or vaccine research, information about the reliability of the predicted parental subtypes and breakpoint positions is valuable. For this reason, we extended the output of jpHMM to include such information in terms of 'uncertainty' regions in the recombination prediction and an interval estimate of the breakpoint. Both types of information are computed based on the posterior probabilities of the subtypes at each query sequence position. Our results show that this extension strongly improves the reliability of the jpHMM recombination prediction. The jpHMM is available online at http://jphmm.gobics.de/.
authors.affiliation: Institut für Mikrobiologie und Genetik, Abteilung für Bioinformatik, Georg-August-Universität Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany.
authors.forename: Anne-Kathrin
authors.initials: AK
authors.lastname: Schultz
authors.forename: Ming
authors.initials: M
authors.lastname: Zhang
authors.forename: Ingo
authors.initials: I
authors.lastname: Bulla
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: D001483:Base Sequence; D053960:DNA Breaks; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D020407:Internet; D008390:Markov Chains; D010802:Phylogeny; D011995:Recombination, Genetic; D015203:Reproducibility of Results; D016415:Sequence Alignment; D012984:Software