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 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.

New application of jpHMM:

• Recombination detection in viruses with circular genomes such as HBV:
  jpHMM is extended to detect recombinations in circular genomes. The method accepts input sequences without assuming a specific origin for the sequence coordinates. It takes into account dependencies between nucleotides at the chosen 5' and 3' end of the linearized version of the genome and is not biased against recombination breakpoints located close to one sequence end.
  For HBV sequences, the circular jpHMM approach is available as a web server. The source code can be downloaded here.

Online submission form for jpHMM.

Download the command line version of jpHMM.
Test data sets that were used in the papers can also be found on the download page.

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-contact@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, I. Bulla, M. Abdou-Chekaraou, E. Gordien, B. Morgenstern, F. Zoulim, P. Dény, M. Stanke. jpHMM: recombination analysis in viruses with circular genomes such as the hepatitis B virus. Nucleic Acids Research, 40:W193-W198. 2012.
  • test data
• 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.

jpHMM is not actively maintained any longer. (Questions or comments? Email contact)
Copyright © 2005-2006 Dept. of Bioinformatics (IMG)