RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints
Identifieur interne : 000018 ( Istex/Corpus ); précédent : 000017; suivant : 000019RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints
Auteurs : Wah-Heng Lee ; Wing-Kin SungSource :
- Lecture Notes in Computer Science [ 0302-9743 ]
Abstract
Abstract: Recombination detection is important before inferring phylogenetic relationships. This will eventually lead to a better understanding of pathogen evolution, more accurate genotyping and advancements in vaccine development. In this paper, we introduce RB-Finder, a fast and accurate distance-based window method to detect recombination in a multiple sequence alignment. Our method introduces a more informative distance measure and a novel weighting strategy to reduce the window size sensitivity problem and hence improve the accuracy of breakpoint detection. Furthermore, our method is faster than existing phylogeny-based methods since we do not need to construct and compare complex phylogenetic trees. When compared with the current best method Pruned-PDM, we are about a few hundred times more efficient. Experimental evaluation of RB-Finder using synthetic and biological datasets showed that our method is more accurate than existing phylogeny-based methods. We also show how our method has potential use in other related applications such as genotyping.
Url:
DOI: 10.1007/978-3-540-71681-5_36
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ISTEX:92F359DBD9A53A096BB64FE8769DD91E35C1C86CLe document en format XML
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This will eventually lead to a better understanding of pathogen evolution, more accurate genotyping and advancements in vaccine development. In this paper, we introduce RB-Finder, a fast and accurate distance-based window method to detect recombination in a multiple sequence alignment. Our method introduces a more informative distance measure and a novel weighting strategy to reduce the window size sensitivity problem and hence improve the accuracy of breakpoint detection. Furthermore, our method is faster than existing phylogeny-based methods since we do not need to construct and compare complex phylogenetic trees. When compared with the current best method Pruned-PDM, we are about a few hundred times more efficient. Experimental evaluation of RB-Finder using synthetic and biological datasets showed that our method is more accurate than existing phylogeny-based methods. 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This will eventually lead to a better understanding of pathogen evolution, more accurate genotyping and advancements in vaccine development. In this paper, we introduce RB-Finder, a fast and accurate distance-based window method to detect recombination in a multiple sequence alignment. Our method introduces a more informative distance measure and a novel weighting strategy to reduce the window size sensitivity problem and hence improve the accuracy of breakpoint detection. Furthermore, our method is faster than existing phylogeny-based methods since we do not need to construct and compare complex phylogenetic trees. When compared with the current best method Pruned-PDM, we are about a few hundred times more efficient. Experimental evaluation of RB-Finder using synthetic and biological datasets showed that our method is more accurate than existing phylogeny-based methods. We also show how our method has potential use in other related applications such as genotyping.</Para></Abstract><KeywordGroup Language="En"><Heading>Keywords</Heading><Keyword>Recombination detection</Keyword><Keyword>sliding window</Keyword><Keyword>phylogeny</Keyword><Keyword> genotyping</Keyword></KeywordGroup></ChapterHeader><NoBody></NoBody></Chapter></Book></Series></Publisher></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>RB-Finder: An Improved Distance-Based Sliding Window Method to Detect Recombination Breakpoints</title></titleInfo><name type="personal"><namePart type="given">Wah-Heng</namePart><namePart type="family">Lee</namePart><affiliation>Genome Institute of Singapore, </affiliation><affiliation>National University of Singapore, </affiliation><affiliation>E-mail: leewhc@gis.a-star.edu.sg</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Wing-Kin</namePart><namePart type="family">Sung</namePart><affiliation>Genome Institute of Singapore, </affiliation><affiliation>National University of Singapore, </affiliation><affiliation>E-mail: ksung@comp.nus.edu.sg</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre displayLabel="OriginalPaper" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" type="conference" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-BFHXPBJJ-3">conference</genre><originInfo><publisher>Springer Berlin Heidelberg</publisher><place><placeTerm type="text">Berlin, Heidelberg</placeTerm></place><dateIssued encoding="w3cdtf">2007</dateIssued><copyrightDate encoding="w3cdtf">2007</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract lang="en">Abstract: Recombination detection is important before inferring phylogenetic relationships. 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We also show how our method has potential use in other related applications such as genotyping.</abstract><subject lang="en"><genre>Keywords</genre><topic>Recombination detection</topic><topic>sliding window</topic><topic>phylogeny</topic><topic>genotyping</topic></subject><relatedItem type="host"><titleInfo><title>Research in Computational Molecular Biology</title><subTitle>11th Annual International Conference, RECOMB 2007, Oakland, CA, USA, April 21-25, 2007. 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Robotics)</topic><topic authority="SpringerSubjectCodes" authorityURI="I23050">Computational Biology/Bioinformatics</topic></subject><identifier type="DOI">10.1007/978-3-540-71681-5</identifier><identifier type="ISBN">978-3-540-71680-8</identifier><identifier type="eISBN">978-3-540-71681-5</identifier><identifier type="ISSN">0302-9743</identifier><identifier type="eISSN">1611-3349</identifier><identifier type="BookTitleID">148814</identifier><identifier type="BookID">978-3-540-71681-5</identifier><identifier type="BookChapterCount">37</identifier><identifier type="BookVolumeNumber">4453</identifier><identifier type="BookSequenceNumber">4453</identifier><part><date>2007</date><detail type="volume"><number>4453</number><caption>vol.</caption></detail><extent unit="pages"><start>518</start><end>532</end></extent></part><recordInfo><recordOrigin>Springer-Verlag Berlin Heidelberg, 2007</recordOrigin></recordInfo></relatedItem><relatedItem type="series"><titleInfo><title>Lecture Notes in Computer Science</title></titleInfo><originInfo><publisher>Springer</publisher><copyrightDate encoding="w3cdtf">2007</copyrightDate><issuance>serial</issuance></originInfo><relatedItem type="constituent"><titleInfo><title>Lecture Notes in Bioinformatics</title></titleInfo><name type="personal"><namePart type="given">Sorin</namePart><namePart type="family">Istrail</namePart><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Pavel</namePart><namePart type="family">Pevzner</namePart><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Michael</namePart><namePart type="given">S.</namePart><namePart type="family">Waterman</namePart><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Terry</namePart><namePart type="family">Speed</namePart><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Haiyan</namePart><namePart type="family">Huang</namePart><role><roleTerm type="text">editor</roleTerm></role></name><genre type="sub-series"></genre><identifier type="ISSN">0302-9743</identifier><identifier type="eISSN">1611-3349</identifier><identifier type="SubSeriesID">5381</identifier></relatedItem><identifier type="ISSN">0302-9743</identifier><identifier type="eISSN">1611-3349</identifier><identifier type="SeriesID">558</identifier><recordInfo><recordOrigin>Springer-Verlag Berlin Heidelberg, 2007</recordOrigin></recordInfo></relatedItem><identifier type="istex">92F359DBD9A53A096BB64FE8769DD91E35C1C86C</identifier><identifier type="ark">ark:/67375/HCB-3BVPS7LJ-B</identifier><identifier type="DOI">10.1007/978-3-540-71681-5_36</identifier><identifier type="ChapterID">36</identifier><identifier type="ChapterID">Chap36</identifier><accessCondition type="use and reproduction" contentType="copyright">Springer-Verlag Berlin Heidelberg, 2007</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-RLRX46XW-4">springer</recordContentSource><recordOrigin>Springer Berlin Heidelberg, 2007</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/HCB-3BVPS7LJ-B/record.json</uri></json:item></metadata></istex></record>Pour manipuler ce document sous Unix (Dilib)
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