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Nucleic Acids Research Advance Access originally published online on May 14, 2009
Nucleic Acids Research 2009 37(Web Server issue):W647-W651; doi:10.1093/nar/gkp371
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Nucleic Acids Research, 2009, Vol. 37, No. suppl_2 W647-W651
© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

Articles

jpHMM: Improving the reliability of recombination prediction in HIV-1

Anne-Kathrin Schultz1, Ming Zhang2,3, Ingo Bulla1, Thomas Leitner2, Bette Korber2,4, Burkhard Morgenstern1 and Mario Stanke1,*

1Institut für Mikrobiologie und Genetik, Abteilung für Bioinformatik, Georg-August-Universität Göttingen, Goldschmidtstr. 1, 37077, Göttingen, Germany, 2T-6, Los Alamos National Laboratory, 3Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 and 4The Santa Fe Institute, Santa Fe, NM 87501, USA

*To whom correspondence should be addressed. Tel: +49 551 3914926; Fax: +49 551 3914929; Email: mstanke{at}gwdg.de, mario.stanke{at}gmail.com

Received February 14, 2009. Revised April 17, 2009. Accepted April 24, 2009.

Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and assigns to each position of the sequence one of the major HIV-1 subtypes. Since incorrect subtype assignment or recombination prediction may lead to wrong conclusions in epidemiological or vaccine research, information about the reliability of the predicted parental subtypes and breakpoint positions is valuable. For this reason, we extended the output of jpHMM to include such information in terms of ‘uncertainty’ regions in the recombination prediction and an interval estimate of the breakpoint. Both types of information are computed based on the posterior probabilities of the subtypes at each query sequence position. Our results show that this extension strongly improves the reliability of the jpHMM recombination prediction. The jpHMM is available online at http://jphmm.gobics.de/.


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