GiRaF: robust, computational identification of influenza reassortments via graph mining
Identifieur interne : 000E77 ( Main/Exploration ); précédent : 000E76; suivant : 000E78GiRaF: robust, computational identification of influenza reassortments via graph mining
Auteurs : Niranjan Nagarajan ; Carl Kingsford [États-Unis]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2010.
Abstract
Reassortments in the influenza virus—a process where strains exchange genetic segments—have been implicated in two out of three pandemics of the 20th century as well as the 2009 H1N1 outbreak. While advances in sequencing have led to an explosion in the number of whole-genome sequences that are available, an understanding of the rate and distribution of reassortments and their role in viral evolution is still lacking. An important factor in this is the paucity of automated tools for confident identification of reassortments from sequence data due to the challenges of analyzing large, uncertain viral phylogenies. We describe here a novel computational method, called GiRaF (Graph-incompatibility-based Reassortment Finder), that robustly identifies reassortments in a fully automated fashion while accounting for uncertainties in the inferred phylogenies. The algorithms behind GiRaF search large collections of Markov chain Monte Carlo (MCMC)-sampled trees for groups of incompatible splits using a fast biclique enumeration algorithm coupled with several statistical tests to identify sets of taxa with differential phylogenetic placement. GiRaF correctly finds known reassortments in human, avian, and swine influenza populations, including the evolutionary events that led to the recent ‘swine flu’ outbreak. GiRaF also identifies several previously unreported reassortments via whole-genome studies to catalog events in H5N1 and swine influenza isolates.
Url:
DOI: 10.1093/nar/gkq1232
PubMed: 21177643
PubMed Central: 3064795
Affiliations:
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">GiRaF: robust, computational identification of influenza reassortments via graph mining</title><author><name sortKey="Nagarajan, Niranjan" sort="Nagarajan, Niranjan" uniqKey="Nagarajan N" first="Niranjan" last="Nagarajan">Niranjan Nagarajan</name><affiliation><nlm:aff id="AFF1">Computational and Mathematical Biology, Genome Institute of Singapore, Singapore-127726,</nlm:aff><wicri:noCountry code="subfield">Singapore-127726</wicri:noCountry></affiliation></author><author><name sortKey="Kingsford, Carl" sort="Kingsford, Carl" uniqKey="Kingsford C" first="Carl" last="Kingsford">Carl Kingsford</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">Center for Bioinformatics and Computational Biology</nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="AFF1">Department of Computer Science, University of Maryland, College Park, MD 20742, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, University of Maryland, College Park, MD 20742</wicri:regionArea><placeName><region type="state">Maryland</region><settlement type="city">College Park (Maryland)</settlement></placeName><orgName type="university">Université du Maryland</orgName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">21177643</idno><idno type="pmc">3064795</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3064795</idno><idno type="RBID">PMC:3064795</idno><idno type="doi">10.1093/nar/gkq1232</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000A33</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000A33</idno><idno type="wicri:Area/Pmc/Curation">000A33</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000A33</idno><idno type="wicri:Area/Pmc/Checkpoint">000944</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000944</idno><idno type="wicri:Area/Ncbi/Merge">000596</idno><idno type="wicri:Area/Ncbi/Curation">000596</idno><idno type="wicri:Area/Ncbi/Checkpoint">000596</idno><idno type="wicri:doubleKey">0305-1048:2010:Nagarajan N:giraf:robust:computational</idno><idno type="wicri:Area/Main/Merge">000E83</idno><idno type="wicri:Area/Main/Curation">000E77</idno><idno type="wicri:Area/Main/Exploration">000E77</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">GiRaF: robust, computational identification of influenza reassortments via graph mining</title><author><name sortKey="Nagarajan, Niranjan" sort="Nagarajan, Niranjan" uniqKey="Nagarajan N" first="Niranjan" last="Nagarajan">Niranjan Nagarajan</name><affiliation><nlm:aff id="AFF1">Computational and Mathematical Biology, Genome Institute of Singapore, Singapore-127726,</nlm:aff><wicri:noCountry code="subfield">Singapore-127726</wicri:noCountry></affiliation></author><author><name sortKey="Kingsford, Carl" sort="Kingsford, Carl" uniqKey="Kingsford C" first="Carl" last="Kingsford">Carl Kingsford</name><affiliation><nlm:aff wicri:cut=" and" id="AFF1">Center for Bioinformatics and Computational Biology</nlm:aff></affiliation><affiliation wicri:level="4"><nlm:aff id="AFF1">Department of Computer Science, University of Maryland, College Park, MD 20742, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, University of Maryland, College Park, MD 20742</wicri:regionArea><placeName><region type="state">Maryland</region><settlement type="city">College Park (Maryland)</settlement></placeName><orgName type="university">Université du Maryland</orgName></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Reassortments in the influenza virus—a process where strains exchange genetic segments—have been implicated in two out of three pandemics of the 20th century as well as the 2009 H1N1 outbreak. While advances in sequencing have led to an explosion in the number of whole-genome sequences that are available, an understanding of the rate and distribution of reassortments and their role in viral evolution is still lacking. An important factor in this is the paucity of automated tools for confident identification of reassortments from sequence data due to the challenges of analyzing large, uncertain viral phylogenies. We describe here a novel computational method, called GiRaF (Graph-incompatibility-based Reassortment Finder), that robustly identifies reassortments in a fully automated fashion while accounting for uncertainties in the inferred phylogenies. The algorithms behind GiRaF search large collections of Markov chain Monte Carlo (MCMC)-sampled trees for groups of incompatible splits using a fast biclique enumeration algorithm coupled with several statistical tests to identify sets of taxa with differential phylogenetic placement. GiRaF correctly finds known reassortments in human, avian, and swine influenza populations, including the evolutionary events that led to the recent ‘swine flu’ outbreak. GiRaF also identifies several previously unreported reassortments via whole-genome studies to catalog events in H5N1 and swine influenza isolates.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Kawaoka, Y" uniqKey="Kawaoka Y">Y Kawaoka</name></author><author><name sortKey="Krauss, S" uniqKey="Krauss S">S Krauss</name></author><author><name sortKey="Webster, Rg" uniqKey="Webster R">RG Webster</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Dawood, Fs" uniqKey="Dawood F">FS Dawood</name></author><author><name sortKey="Jain, S" uniqKey="Jain S">S Jain</name></author><author><name sortKey="Finelli, L" uniqKey="Finelli L">L Finelli</name></author><author><name sortKey="Shaw, Mw" uniqKey="Shaw M">MW Shaw</name></author><author><name sortKey="Lindstrom, S" uniqKey="Lindstrom S">S Lindstrom</name></author><author><name sortKey="Garten, Rj" uniqKey="Garten R">RJ Garten</name></author><author><name 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D" uniqKey="Paraskevis D">D Paraskevis</name></author><author><name sortKey="Deforche, K" uniqKey="Deforche K">K Deforche</name></author><author><name sortKey="Lemey, P" uniqKey="Lemey P">P Lemey</name></author><author><name sortKey="Magiorkinis, G" uniqKey="Magiorkinis G">G Magiorkinis</name></author><author><name sortKey="Hatzakis, A" uniqKey="Hatzakis A">A Hatzakis</name></author><author><name sortKey="Vandamme, Am" uniqKey="Vandamme A">AM Vandamme</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>États-Unis</li></country><region><li>Maryland</li></region><settlement><li>College Park (Maryland)</li></settlement><orgName><li>Université du Maryland</li></orgName></list><tree><noCountry><name sortKey="Nagarajan, Niranjan" sort="Nagarajan, Niranjan" uniqKey="Nagarajan N" first="Niranjan" last="Nagarajan">Niranjan Nagarajan</name></noCountry><country name="États-Unis"><region name="Maryland"><name sortKey="Kingsford, Carl" 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