jpHMM [Program limitations]

Limitations of the jpHMM online tool for HIV-1

• HIV-1 subtypes H, J, K
  
  Sometimes this tool is not sensitive enough to detect HIV-1 subtype H, J, K, as only few full-length genome sequences of these subtypes are available worldwide. In this case, the jpHMM results should be compared with those of other HIV-1 subtyping tools, for example RIP.
  
  
• Partially missing HIV-1 subtype assignment
  
  It may happen that parts of the query HIV-1 sequence are not assigned to any HIV-1 subtype. One reason for this problem may be the computer memory used by jpHMM. In this case please
  • contact us (jphmm-contact@gobics.de), so that we can run the program locally using a larger search space
    
  • or download the command line version of jpHMM and run the program using a smaller(!) value for the 'beam_width' (option -B).
    
• 3' end of full-length HIV-1 genomes
  
  For full-length HIV-1 genome sequences jpHMM sometimes predicts a jump to subtype B at the 3' end. This recombination breakpoint can often be incorrect.

Since we are still working on the improvement of jpHMM, we would really appreciate your feedback if you encounter further problems or limitations of the program.

References

• 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.
• 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
• 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.

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