jpHMM [Main page]

jpHMM

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 genomic recombinations in HIV-1 and HBV.

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.

New features of the Web Interface:

• The output of jpHMM now includes information about the reliability of the predicted recombination breakpoints and parental subtypes in the form of uncertainty regions and breakpoint intervals.
  (The original recombination prediction containing precise breakpoint positions is still available.)
• For HIV: we now use HXB2 numbering to predefine a local alignment of the query sequence to the multiple sequence alignment. This reduces the search space for jpHMM and, as a consequence, the runtime of jpHMM, especially for short sequences.
• For HIV: the alignment of the query sequence to the HXB2 sequence, which is part of the multiple alignment we use to build the model, defined by jpHMM is now available. This provides additional information about the quality of the jpHMM prediction.

Online submission form for jpHMM.

Download the command line version of jpHMM.

This project is a collaborative effort between the Department of Bioinformatics of the University of Göttingen and the Los Alamos HIV Sequence Database Group.
The application of jpHMM to HBV was developed in collaboration with the Laboratoire INSERM U871 in Lyon and the Laboratoire associé au Centre National de Référence des hépatites B, C et delta, UFR Santé Médecine Biologie Humaine, at the Université Paris 13.

In case of questions concerning jpHMM algorithm details or bugs, please contact jphmm-web@gobics.de. For HIV-1 subtyping questions, please contact seq-info@lanl.gov.

References

Please cite one of the following papers if you use this tool in your publication (a list of all references can be found here):

• A.-K. Schultz, M. Zhang, I. Bulla, T. Leitner, B. Korber, B. Morgenstern, M. Stanke. jpHMM: Improving the reliability of recombination prediction in HIV-1. Nucleic Acids Research, 37:W647-51. 2009
  • test data
• M. Zhang, A.-K. Schultz, C. Calef, C. Kuiken, T. Leitner, B. Korber, B. Morgenstern, M. Stanke. jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1. Nucleic Acids Research, 34:W463-5. 2006.
  
• A.-K. Schultz, M. Zhang, T. Leitner, C. Kuiken, B. Korber, B. Morgenstern, M. Stanke. A Jumping Profile Hidden Markov Model and Applications to Recombination Sites in HIV and HCV Genomes. BMC Bioinformatics 7:265. 2006.
  
  • Sequence test sets used in Fig.8. Inter-subtype sequences; Inter sub-subtype sequences;
  • Raw test result for plotting Fig.8. Inter-subtype sequence results; Inter sub-subtype sequence results.

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Copyright © 2005-2006 Dept. of Bioinformatics (IMG)