University of Göttingen  |  Faculty of Biology  |  Institute of Microbiology and Genetics  |  Dept. of Bioinformatics

jpHMM [Help]

What does jpHMM do?

jpHMM is a probabilistic approach to predict recombinations in viral genome sequences such as HIV-1 and HBV genomes. On the basis of a multiple sequence alignment subdivided into the major subtypes, jpHMM determines whether a query sequence is a recombinant. If so, it estimates the recombination breakpoints and assigns to each segment in between two breakpoints a parental subtype among the given subtypes. Additionally, an 'interval' estimate for each predicted breakpoint (breakpoint interval) and a tagging of regions in which the model is uncertain about the predicted subtype (uncertainty regions) are given.

The jpHMM web server is available for HIV-1 and HBV.

Input and job submission

jpHMM provides an easy-to-use submission interface for HIV-1 as well as HBV sequences. For HIV-1, you can paste or upload up to 5 full-length, for HBV, up to 20 full-length genomic sequences or fragments at a time in FASTA format. Alternatively, you can select an example sequence (by clicking on 'sample input'), which is stored on the jpHMM server, but will be processed like any other input.
Optionally, you can provide an e-mail address to receive a hyperlink to the result page by e-mail.

After pasting or uploading the sequences, press the 'RUN jpHMM' button to start the processing.

Output and interpretation of results

A hyperlink to the result page is given and can be bookmarked. The results are stored on the server for seven days.
An example output with active links to the result files is given for HIV-1 and HBV. Also, sample outputs in png format are provided for HIV-1 and HBV.

The results contain


All result files can be downloaded. In addition to the figures, the predicted recombination and the posterior probabilities can be downloaded in text format. Additionally, a file with the pairwise alignment of each query sequence to the reference genome (which is part of the multiple alignment) determined with jpHMM can be downloaded at the end of the result page.


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

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