Profiling and Searching for RNA Pseudoknot Structures in Genomes
Identifieur interne : 000137 ( Istex/Corpus ); précédent : 000136; suivant : 000138Profiling and Searching for RNA Pseudoknot Structures in Genomes
Auteurs : Chunmei Liu ; Yinglei Song ; Russell L. Malmberg ; Liming CaiSource :
- Lecture Notes in Computer Science [ 0302-9743 ]
Abstract
Abstract: A new method is developed that can profile and efficiently search for pseudoknot structures in noncoding RNA genes. It profiles interleaving stems in pseudoknot structures with independent Covariance Model (CM) components. The statistical alignment score for searching is obtained by combining the alignment scores from all CM components. Our experiments show that the model can achieve excellent accuracy on both random and biological data. The efficiency achieved by the method makes it possible to search for the pseudoknot structures in genomes of a variety of organisms.
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DOI: 10.1007/11428848_123
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ISTEX:AC899D300C3DACC0FDFE40719D596A57B90B997CLe document en format XML
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It profiles interleaving stems in pseudoknot structures with independent Covariance Model (CM) components. The statistical alignment score for searching is obtained by combining the alignment scores from all CM components. Our experiments show that the model can achieve excellent accuracy on both random and biological data. 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University</OrgName><OrgAddress><City>Pittsburgh</City><State>PA</State><Country>USA</Country></OrgAddress></Affiliation><Affiliation ID="Aff3"><OrgName>University of Surrey</OrgName><OrgAddress><City>Guildford</City><Country>UK</Country></OrgAddress></Affiliation><Affiliation ID="Aff4"><OrgName>Cornell University</OrgName><OrgAddress><City>Ithaca</City><State>NY</State><Country>USA</Country></OrgAddress></Affiliation><Affiliation ID="Aff5"><OrgName>ETH Zurich</OrgName><OrgAddress><Country>Switzerland</Country></OrgAddress></Affiliation><Affiliation ID="Aff6"><OrgName>Stanford University</OrgName><OrgAddress><City>CA</City><Country>USA</Country></OrgAddress></Affiliation><Affiliation ID="Aff7"><OrgName>Weizmann Institute of Science</OrgName><OrgAddress><City>Rehovot</City><Country>Israel</Country></OrgAddress></Affiliation><Affiliation ID="Aff8"><OrgName>University of Bern</OrgName><OrgAddress><Country>Switzerland</Country></OrgAddress></Affiliation><Affiliation ID="Aff9"><OrgName>Indian Institute of Technology</OrgName><OrgAddress><City>Madras</City><Country>India</Country></OrgAddress></Affiliation><Affiliation ID="Aff10"><OrgName>University of Dortmund</OrgName><OrgAddress><Country>Germany</Country></OrgAddress></Affiliation><Affiliation ID="Aff11"><OrgName>Massachusetts Institute of Technology</OrgName><OrgAddress><City>MA</City><Country>USA</Country></OrgAddress></Affiliation><Affiliation ID="Aff12"><OrgName>New York University</OrgName><OrgAddress><City>NY</City><Country>USA</Country></OrgAddress></Affiliation><Affiliation ID="Aff13"><OrgName>University of California</OrgName><OrgAddress><City>Berkeley</City><State>CA</State><Country>USA</Country></OrgAddress></Affiliation><Affiliation ID="Aff14"><OrgName>Rice University</OrgName><OrgAddress><City>Houston</City><State>TX</State><Country>USA</Country></OrgAddress></Affiliation><Affiliation ID="Aff15"><OrgName>Max-Planck Institute of Computer Science</OrgName><OrgAddress><City>Saarbruecken</City><Country>Germany</Country></OrgAddress></Affiliation></EditorGroup></SeriesHeader><Book Language="En"><BookInfo BookProductType="Proceedings" ContainsESM="No" Language="En" MediaType="eBook" NumberingDepth="2" NumberingStyle="ContentOnly" OutputMedium="All" TocLevels="0"><BookID>978-3-540-32114-9</BookID><BookTitle>Computational Science – ICCS 2005</BookTitle><BookSubTitle>5th International Conference, Atlanta, GA, USA, May 22-25, 2005. Proceedings, Part II</BookSubTitle><BookVolumeNumber>3515</BookVolumeNumber><BookSequenceNumber>3515</BookSequenceNumber><BookDOI>10.1007/b136571</BookDOI><BookTitleID>118307</BookTitleID><BookPrintISBN>978-3-540-26043-1</BookPrintISBN><BookElectronicISBN>978-3-540-32114-9</BookElectronicISBN><BookChapterCount>136</BookChapterCount><BookCopyright><CopyrightHolderName>Springer-Verlag Berlin Heidelberg</CopyrightHolderName><CopyrightYear>2005</CopyrightYear></BookCopyright><BookSubjectGroup><BookSubject Code="I" Type="Primary">Computer Science</BookSubject><BookSubject Code="I14002" Priority="1" Type="Secondary">Software Engineering/Programming and Operating Systems</BookSubject><BookSubject Code="I16005" Priority="2" Type="Secondary">Theory of Computation</BookSubject><BookSubject Code="I1701X" Priority="3" Type="Secondary">Numeric Computing</BookSubject><BookSubject Code="I18008" Priority="4" Type="Secondary">Information Systems and Communication Service</BookSubject><BookSubject Code="I21025" Priority="5" Type="Secondary">Simulation and Modeling</BookSubject><BookSubject Code="I22005" Priority="6" Type="Secondary">Computer Imaging, Vision, Pattern Recognition and Graphics</BookSubject><SubjectCollection Code="SUCO11645">Computer Science</SubjectCollection></BookSubjectGroup><BookContext><SeriesID>558</SeriesID></BookContext></BookInfo><BookHeader><EditorGroup><Editor AffiliationIDS="Aff16"><EditorName DisplayOrder="Western"><GivenName>Vaidy</GivenName><GivenName>S.</GivenName><FamilyName>Sunderam</FamilyName></EditorName><Contact><Email>vss@emory.edu</Email></Contact></Editor><Editor AffiliationIDS="Aff17"><EditorName DisplayOrder="Western"><GivenName>Geert</GivenName><GivenName>Dick</GivenName><Particle>van</Particle><FamilyName>Albada</FamilyName></EditorName><Contact><Email>dick@science.uva.nl</Email></Contact></Editor><Editor AffiliationIDS="Aff18"><EditorName DisplayOrder="Western"><GivenName>Peter</GivenName><GivenName>M.</GivenName><GivenName>A.</GivenName><FamilyName>Sloot</FamilyName></EditorName><Contact><Email>sloot@science.uva.nl</Email></Contact></Editor><Editor AffiliationIDS="Aff19"><EditorName DisplayOrder="Western"><GivenName>Jack</GivenName><GivenName>J.</GivenName><FamilyName>Dongarra</FamilyName></EditorName><Contact><Email>dongarra@eecs.utk.edu</Email></Contact></Editor><Affiliation ID="Aff16"><OrgDivision>Department of Mathematics and Computer Science</OrgDivision><OrgName>Emory University</OrgName><OrgAddress><City>Atlanta</City><State>Georgia</State><Country>USA</Country></OrgAddress></Affiliation><Affiliation ID="Aff17"><OrgDivision>Department of Mathematics and Computer Science</OrgDivision><OrgName>University of Amsterdam</OrgName><OrgAddress><Street>Kruislaan 403</Street><Postcode>1098</Postcode><City>Amsterdam</City><State>SJ</State><Country>The Netherlands</Country></OrgAddress></Affiliation><Affiliation ID="Aff18"><OrgDivision>Faculty of Sciences, Section of Computational Science</OrgDivision><OrgName>University of Amsterdam</OrgName><OrgAddress><Street>Kruislaan 403</Street><Postcode>1098</Postcode><City>Amsterdam</City><State>SJ</State><Country>The Netherlands</Country></OrgAddress></Affiliation><Affiliation ID="Aff19"><OrgDivision>Computer Science Department</OrgDivision><OrgName>University of Tennessee</OrgName><OrgAddress><Postcode>37996-3450</Postcode><City>TN</City><State>Knoxville</State><Country>USA</Country></OrgAddress></Affiliation></EditorGroup></BookHeader><Part ID="Part9"><PartInfo TocLevels="0"><PartID>9</PartID><PartNumber>2005</PartNumber><PartSequenceNumber>9</PartSequenceNumber><PartTitle>International Workshop on Bioinformatics Research and Applications</PartTitle><PartChapterCount>24</PartChapterCount><PartContext><SeriesID>558</SeriesID><BookTitle>Computational Science – ICCS 2005</BookTitle></PartContext></PartInfo><Chapter ID="Chap123" Language="En"><ChapterInfo ChapterType="OriginalPaper" ContainsESM="No" NumberingDepth="2" NumberingStyle="ContentOnly" TocLevels="0"><ChapterID>123</ChapterID><ChapterDOI>10.1007/11428848_123</ChapterDOI><ChapterSequenceNumber>123</ChapterSequenceNumber><ChapterTitle Language="En">Profiling and Searching for RNA Pseudoknot Structures in Genomes</ChapterTitle><ChapterFirstPage>968</ChapterFirstPage><ChapterLastPage>975</ChapterLastPage><ChapterCopyright><CopyrightHolderName>Springer-Verlag Berlin Heidelberg</CopyrightHolderName><CopyrightYear>2005</CopyrightYear></ChapterCopyright><ChapterGrants Type="Regular"><MetadataGrant Grant="OpenAccess"></MetadataGrant><AbstractGrant Grant="OpenAccess"></AbstractGrant><BodyPDFGrant Grant="Restricted"></BodyPDFGrant><BodyHTMLGrant Grant="Restricted"></BodyHTMLGrant><BibliographyGrant Grant="Restricted"></BibliographyGrant><ESMGrant Grant="Restricted"></ESMGrant></ChapterGrants><ChapterContext><SeriesID>558</SeriesID><PartID>9</PartID><BookID>978-3-540-32114-9</BookID><BookTitle>Computational Science – ICCS 2005</BookTitle></ChapterContext></ChapterInfo><ChapterHeader><AuthorGroup><Author AffiliationIDS="Aff20"><AuthorName DisplayOrder="Western"><GivenName>Chunmei</GivenName><FamilyName>Liu</FamilyName></AuthorName><Contact><Email>chunmei@cs.uga.edu</Email></Contact></Author><Author AffiliationIDS="Aff20"><AuthorName DisplayOrder="Western"><GivenName>Yinglei</GivenName><FamilyName>Song</FamilyName></AuthorName><Contact><Email>song@cs.uga.edu</Email></Contact></Author><Author AffiliationIDS="Aff21"><AuthorName DisplayOrder="Western"><GivenName>Russell</GivenName><GivenName>L.</GivenName><FamilyName>Malmberg</FamilyName></AuthorName><Contact><Email>russell@plantbio.uga.edu</Email></Contact></Author><Author AffiliationIDS="Aff20"><AuthorName DisplayOrder="Western"><GivenName>Liming</GivenName><FamilyName>Cai</FamilyName></AuthorName><Contact><Email>cai@cs.uga.edu</Email></Contact></Author><Affiliation ID="Aff20"><OrgDivision>Department of Computer Science</OrgDivision><OrgName>University of Georgia</OrgName><OrgAddress><City>Athens</City><State>GA</State><Postcode>30602</Postcode><Country>USA</Country></OrgAddress></Affiliation><Affiliation ID="Aff21"><OrgDivision>Department of Plant Biology</OrgDivision><OrgName>University of Georgia</OrgName><OrgAddress><City>Athens</City><State>GA</State><Postcode>30602</Postcode><Country>USA</Country></OrgAddress></Affiliation></AuthorGroup><Abstract ID="Abs1" Language="En"><Heading>Abstract</Heading><Para>A new method is developed that can profile and efficiently search for pseudoknot structures in noncoding RNA genes. It profiles interleaving stems in pseudoknot structures with independent Covariance Model (CM) components. The statistical alignment score for searching is obtained by combining the alignment scores from all CM components. Our experiments show that the model can achieve excellent accuracy on both random and biological data. The efficiency achieved by the method makes it possible to search for the pseudoknot structures in genomes of a variety of organisms.</Para></Abstract></ChapterHeader><NoBody></NoBody></Chapter></Part></Book></Series></Publisher></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Profiling and Searching for RNA Pseudoknot Structures in Genomes</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Profiling and Searching for RNA Pseudoknot Structures in Genomes</title></titleInfo><name type="personal"><namePart type="given">Chunmei</namePart><namePart type="family">Liu</namePart><affiliation>Department of Computer Science, University of Georgia, 30602, Athens, GA, USA</affiliation><affiliation>E-mail: chunmei@cs.uga.edu</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Yinglei</namePart><namePart type="family">Song</namePart><affiliation>Department of Computer Science, University of Georgia, 30602, Athens, GA, USA</affiliation><affiliation>E-mail: song@cs.uga.edu</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Russell</namePart><namePart type="given">L.</namePart><namePart type="family">Malmberg</namePart><affiliation>Department of Plant Biology, University of Georgia, 30602, Athens, GA, USA</affiliation><affiliation>E-mail: russell@plantbio.uga.edu</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Liming</namePart><namePart type="family">Cai</namePart><affiliation>Department of Computer Science, University of Georgia, 30602, Athens, GA, USA</affiliation><affiliation>E-mail: cai@cs.uga.edu</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">2005</dateIssued><copyrightDate encoding="w3cdtf">2005</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract lang="en">Abstract: A new method is developed that can profile and efficiently search for pseudoknot structures in noncoding RNA genes. It profiles interleaving stems in pseudoknot structures with independent Covariance Model (CM) components. The statistical alignment score for searching is obtained by combining the alignment scores from all CM components. Our experiments show that the model can achieve excellent accuracy on both random and biological data. The efficiency achieved by the method makes it possible to search for the pseudoknot structures in genomes of a variety of organisms.</abstract><relatedItem type="host"><titleInfo><title>Computational Science – ICCS 2005</title><subTitle>5th International Conference, Atlanta, GA, USA, May 22-25, 2005. Proceedings, Part II</subTitle></titleInfo><name type="personal"><namePart type="given">Vaidy</namePart><namePart type="given">S.</namePart><namePart type="family">Sunderam</namePart><affiliation>Department of Mathematics and Computer Science, Emory University, Atlanta, Georgia, USA</affiliation><affiliation>E-mail: vss@emory.edu</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Geert</namePart><namePart type="given">Dick</namePart><namePart type="family">van Albada</namePart><affiliation>Department of Mathematics and Computer Science, University of Amsterdam, Kruislaan 403, 1098, Amsterdam, SJ, The Netherlands</affiliation><affiliation>E-mail: dick@science.uva.nl</affiliation><role><roleTerm type="text">editor</roleTerm></role></name><name type="personal"><namePart type="given">Peter</namePart><namePart type="given">M.</namePart><namePart type="given">A.</namePart><namePart 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