Improving the reliability of the jpHMM recombination prediction in HIV

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Accurate classification of HIV and the identification of recombinants, including precise breakpoint definitions, is of crucial importance for epidemiological monitoring and the design of potential drugs. Recently we developed jpHMM, a new method to detect recombinations in HIV-l genomes. jpHMM predicts phylogenetic recombination breakpoints in a query sequence and assigns to each segment of the sequence one of the major HIV-l subtypes. For the user the reliability of the predicted breakpoint positions and parental subtypes is most important. For this reason we extended the output of jpHMM to include the information on regions where the model is 'uncertain' about the ... continued below

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Zhang, Ming; Letiner, Thomas K & Korber, Bette T January 1, 2008.

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Accurate classification of HIV and the identification of recombinants, including precise breakpoint definitions, is of crucial importance for epidemiological monitoring and the design of potential drugs. Recently we developed jpHMM, a new method to detect recombinations in HIV-l genomes. jpHMM predicts phylogenetic recombination breakpoints in a query sequence and assigns to each segment of the sequence one of the major HIV-l subtypes. For the user the reliability of the predicted breakpoint positions and parental subtypes is most important. For this reason we extended the output of jpHMM to include the information on regions where the model is 'uncertain' about the parental subtype and an interval estimate of the breakpoint. This information is determined using the posterior probabilities of the subtypes at each query sequence position.

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  • Journal Name: Bioinformatics Journal

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  • Report No.: LA-UR-08-07959
  • Report No.: LA-UR-08-7959
  • Grant Number: AC52-06NA25396
  • Office of Scientific & Technical Information Report Number: 956656
  • Archival Resource Key: ark:/67531/metadc930245

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  • January 1, 2008

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  • Nov. 13, 2016, 7:26 p.m.

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  • Dec. 12, 2016, 12:15 p.m.

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Zhang, Ming; Letiner, Thomas K & Korber, Bette T. Improving the reliability of the jpHMM recombination prediction in HIV, article, January 1, 2008; [New Mexico]. (digital.library.unt.edu/ark:/67531/metadc930245/: accessed November 20, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.