Abstract:
: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/.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Schultz AK,Zhang M,Bulla I,Leitner T,Korber B,Morgenstern B,Stanke Mdoi
10.1093/nar/gkp371subject
Has Abstractpub_date
2009-07-01 00:00:00pages
W647-51issue
Web Server issueeissn
0305-1048issn
1362-4962pii
gkp371journal_volume
37pub_type
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