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

被引：137

作者：

Schultz, Anne-Kathrin ^{[1
]}

Zhang, Ming ^{[2
,3
]}

Bulla, Ingo ^{[1
]}

Leitner, Thomas ^{[2
]}

Korber, Bette ^{[2
,4
]}

Morgenstern, Burkhard ^{[1
]}

Stanke, Mario ^{[1
]}

机构：

[1] Univ Gottingen, Abt Bioinformat, Inst Mikrobiol & Genet, D-37077 Gottingen, Germany

[2] Los Alamos Natl Lab, T6, Los Alamos, NM 87545 USA

[3] Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA

[4] Santa Fe Inst, Santa Fe, NM 87501 USA

来源：

NUCLEIC ACIDS RESEARCH | 2009年 / 37卷

关键词：

MULTIPLE ALIGNMENTS; SEQUENCES; GENOMES; TOPALI; VIRUS;

D O I：

10.1093/nar/gkp371

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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/.

引用

页码：W647 / W651

页数：5

共 15 条

[1] An automated genotyping system for analysis of HIV-1 and other microbial sequences [J].

de Oliveira, T ;

Deforche, K ;

Cassol, S ;

Salminen, M ;

Paraskevis, D ;

Seebregts, C ;

Snoeck, J ;

van Rensburg, EJ ;

Wensing, AMJ ;

van de Vijver, DA ;

Boucher, CA ;

Camacho, R ;

Vandamme, AM .

BIOINFORMATICS, 2005, 21 (19) :3797-3800

[2]

Durbin R., 1998, Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids

[3] Profile hidden Markov models [J].

Eddy, SR .

BIOINFORMATICS, 1998, 14 (09) :755-763

[4] cBrother: relaxing parental tree assumptions for Bayesian recombination detection [J].

Fang, Fang ;

Ding, Jing ;

Minin, Vladimir N. ;

Suchard, Marc A. ;

Dorman, Karin S. .

BIOINFORMATICS, 2007, 23 (04) :507-508

[5]

Foley B.T., 1998, HUMAN RETROVIRUSES A, P102

[6] Detection of HIV-1 subtypes, recombinants, and dual infections in east Africa by a multi-region hybridization assay [J].

Hoelscher, M ;

Dowling, WE ;

Sanders-Buell, E ;

Carr, JK ;

Harris, ME ;

Thomschke, A ;

Robb, ML ;

Birx, DL ;

McCutchan, FE .

AIDS, 2002, 16 (15) :2055-2064

[7] Classification of hepatitis C virus and human immunodeficiency virus-1 sequences with the branching index [J].

Hraber, Peter ;

Kuiken, Carla ;

Waugh, Mark ;

Geer, Shaun ;

Bruno, William J. ;

Leitner, Thomas .

JOURNAL OF GENERAL VIROLOGY, 2008, 89 :2098-2107

[8] Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination [J].

Lole, KS ;

Bollinger, RC ;

Paranjape, RS ;

Gadkari, D ;

Kulkarni, SS ;

Novak, NG ;

Ingersoll, R ;

Sheppard, HW ;

Ray, SC .

JOURNAL OF VIROLOGY, 1999, 73 (01) :152-160

[9] Recco: recombination analysis using cost optimization [J].

Maydt, J ;

Lengauer, T .

BIOINFORMATICS, 2006, 22 (09) :1064-1071

[10] TOPALi: software for automatic identification of recombinant sequences within DNA multiple alignments [J].

Milne, I ;

Wright, F ;

Rowe, G ;

Marshall, DF ;

Husmeier, D ;

McGuire, G .

BIOINFORMATICS, 2004, 20 (11) :1806-1807

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