Please use the following form to submit your HBV sequence(s):
(up to 20 full-length HBV genome sequences)
Please note that only nucleotide HBV sequences in FASTA format are accepted.
Information about the usage of the web server and the interpretation of the results can be found here.
Information in the result: [output sample]
- Sequence genotype;
- Predicted recombinant breakpoint position/interval which is in two forms:
1. based on input sequence's position number;
2. given relative to the HBV reference genome AM282986.
(Information about breakpoint intervals and uncertainty regions is given here) - Genome map (with positions in the reference genome AM282986 as coordinates)
in a circular form
,
including a plot of the posterior probabilities for each genotype at each sequence position;
Available in png and svg format; -
Links to download
- the predicted recombination containing exact breakpoint positions and including uncertainty regions and breakpoint intervals;
- the posterior probabilities of the genotypes at each sequence position;
- the pairwise alignment of each query sequence to the reference genome (AM282986) defined by jpHMM (for all sequences at the end of the page (one file)): Upper-case letters are considered to be aligned, lower-case letters are NOT aligned. '.' denote identical residues, '-' gaps. Numbers x and y given in the output (">AM282986 x y") indicate the start (x) and end (y) position in the reference genome (AM282986). Negative numbers x indicate an offset of x to the reference origin.
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
- 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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Copyright © 2005-2006 Dept. of Bioinformatics (IMG)