jpHMM (jumping profile Hidden Markov Model) is a probabilistic approach to compare a sequence to a multiple alignment of a sequence family. The jpHMM web server at GOBICS is a tool for the detection of recombinations in HIV-1 and hepatitis B virus (HBV) genomes. For a query sequence phylogenetic recombination breakpoints are predicted and each region of the sequence is assigned to one HIV-1 subtype/HBV genotype. This prediction is based on a pre-calculated multiple alignment of the major HIV-1 subtypes/HBV genotypes. A detailed description of the algorithm and some information about the evaluation can be found here. For information about the output format please see the online submission page

References in zbMATH (referenced in 4 articles )

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  1. Schultz, Anne-Kathrin: Improvement of the jpHMM approach to recombination detection in viral genomes and its applications to HIV and HBV. (2011)
  2. Lemey, Philippe; Lott, Martin; Martin, Darren P.; Moulton, Vincent: Identifying recombinants in human and primate immunodeficiency virus sequence alignments using quartet scanning (2009) ioport
  3. Schultz, Anne-Kathrin; Zhang, Ming; Bulla, Ingo; Leitner, Thomas; Korber, Bette; Morgenstern, Burkhard; Stanke, Mario: Jphmm: improving the reliability of recombination prediction in HIV-1 (2009) ioport
  4. Zhang, Ming; Schultz, Anne-Kathrin; Calef, Charles; Kuiken, Carla; Leitner, Thomas; Korber, Bette; Morgenstern, Burkhard; Stanke, Mario: Jphmm at GOBICS: a web server to detect genomic recombinations in HIV-1. (2006) ioport

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