jpHMM: improving the reliability of recombination prediction in HIV-1.
jpHMM: improving the reliability of recombination prediction in HIV-1.
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DOI：
10.1093/nar/gkp371
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发表时间：
2009-07
影响因子：
14.9
通讯作者：
Stanke M
中科院分区：
文献类型：
--
作者：
Schultz AK;Zhang M;Bulla I;Leitner T;Korber B;Morgenstern B;Stanke M
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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通讯作者：
Stanke M