Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.
Identifieur interne : 002241 ( PubMed/Curation ); précédent : 002240; suivant : 002242Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.
Auteurs : Georgios S. Vernikos [Royaume-Uni] ; Julian ParkhillSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2006.
Descripteurs français
- KwdFr :
- MESH :
- génétique : ADN bactérien, Facteurs de virulence, Génome bactérien, Ilots génomiques, Salmonella, Transfert horizontal de gène, Virulence.
- pathogénicité : Salmonella.
- Algorithmes, Évolution biologique.
English descriptors
- KwdEn :
- MESH :
- chemical , genetics : DNA, Bacterial, Virulence Factors.
- genetics : Gene Transfer, Horizontal, Genome, Bacterial, Genomic Islands, Salmonella, Virulence.
- pathogenicity : Salmonella.
- Algorithms, Biological Evolution.
Abstract
There is a growing literature on the detection of Horizontal Gene Transfer (HGT) events by means of parametric, non-comparative methods. Such approaches rely only on sequence information and utilize different low and high order indices to capture compositional deviation from the genome backbone; the superiority of the latter over the former has been shown elsewhere. However even high order k-mers may be poor estimators of HGT, when insufficient information is available, e.g. in short sliding windows. Most of the current HGT prediction methods require pre-existing annotation, which may restrict their application on newly sequenced genomes.
DOI: 10.1093/bioinformatics/btl369
PubMed: 16837528
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Vernikos</name><affiliation wicri:level="1"><nlm:affiliation>The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA, UK. gsv@sanger.ac.uk</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Parkhill, Julian" sort="Parkhill, Julian" uniqKey="Parkhill J" first="Julian" last="Parkhill">Julian Parkhill</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2006">2006</date><idno type="RBID">pubmed:16837528</idno><idno type="pmid">16837528</idno><idno type="doi">10.1093/bioinformatics/btl369</idno><idno type="wicri:Area/PubMed/Corpus">002241</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">002241</idno><idno type="wicri:Area/PubMed/Curation">002241</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">002241</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.</title><author><name sortKey="Vernikos, Georgios S" sort="Vernikos, Georgios S" uniqKey="Vernikos G" first="Georgios S" last="Vernikos">Georgios S. Vernikos</name><affiliation wicri:level="1"><nlm:affiliation>The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA, UK. gsv@sanger.ac.uk</nlm:affiliation><country xml:lang="fr">Royaume-Uni</country><wicri:regionArea>The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA</wicri:regionArea></affiliation></author><author><name sortKey="Parkhill, Julian" sort="Parkhill, Julian" uniqKey="Parkhill J" first="Julian" last="Parkhill">Julian Parkhill</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2006" type="published">2006</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Biological Evolution</term><term>DNA, Bacterial (genetics)</term><term>Gene Transfer, Horizontal (genetics)</term><term>Genome, Bacterial (genetics)</term><term>Genomic Islands (genetics)</term><term>Salmonella (genetics)</term><term>Salmonella (pathogenicity)</term><term>Virulence (genetics)</term><term>Virulence Factors (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>ADN bactérien (génétique)</term><term>Algorithmes</term><term>Facteurs de virulence (génétique)</term><term>Génome bactérien (génétique)</term><term>Ilots génomiques (génétique)</term><term>Salmonella (génétique)</term><term>Salmonella (pathogénicité)</term><term>Transfert horizontal de gène (génétique)</term><term>Virulence (génétique)</term><term>Évolution biologique</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA, Bacterial</term><term>Virulence Factors</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Gene Transfer, Horizontal</term><term>Genome, Bacterial</term><term>Genomic Islands</term><term>Salmonella</term><term>Virulence</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>ADN bactérien</term><term>Facteurs de virulence</term><term>Génome bactérien</term><term>Ilots génomiques</term><term>Salmonella</term><term>Transfert horizontal de gène</term><term>Virulence</term></keywords><keywords scheme="MESH" qualifier="pathogenicity" xml:lang="en"><term>Salmonella</term></keywords><keywords scheme="MESH" qualifier="pathogénicité" xml:lang="fr"><term>Salmonella</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Biological Evolution</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Évolution biologique</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">There is a growing literature on the detection of Horizontal Gene Transfer (HGT) events by means of parametric, non-comparative methods. Such approaches rely only on sequence information and utilize different low and high order indices to capture compositional deviation from the genome backbone; the superiority of the latter over the former has been shown elsewhere. However even high order k-mers may be poor estimators of HGT, when insufficient information is available, e.g. in short sliding windows. Most of the current HGT prediction methods require pre-existing annotation, which may restrict their application on newly sequenced genomes.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" Owner="NLM"><PMID Version="1">16837528</PMID><DateCompleted><Year>2006</Year><Month>09</Month><Day>25</Day></DateCompleted><DateRevised><Year>2010</Year><Month>11</Month><Day>18</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>22</Volume><Issue>18</Issue><PubDate><Year>2006</Year><Month>Sep</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Interpolated variable order motifs for identification of horizontally acquired DNA: revisiting the Salmonella pathogenicity islands.</ArticleTitle><Pagination><MedlinePgn>2196-203</MedlinePgn></Pagination><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">There is a growing literature on the detection of Horizontal Gene Transfer (HGT) events by means of parametric, non-comparative methods. Such approaches rely only on sequence information and utilize different low and high order indices to capture compositional deviation from the genome backbone; the superiority of the latter over the former has been shown elsewhere. However even high order k-mers may be poor estimators of HGT, when insufficient information is available, e.g. in short sliding windows. Most of the current HGT prediction methods require pre-existing annotation, which may restrict their application on newly sequenced genomes.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">We introduce a novel computational method, Interpolated Variable Order Motifs (IVOMs), which exploits compositional biases using variable order motif distributions and captures more reliably the local composition of a sequence compared with fixed-order methods. For optimal localization of the boundaries of each predicted region, a second order, two-state hidden Markov model (HMM) is implemented in a change-point detection framework. We applied the IVOM approach to the genome of Salmonella enterica serovar Typhi CT18, a well-studied prokaryote in terms of HGT events, and we show that the IVOMs outperform state-of-the-art low and high order motif methods predicting not only the already characterized Salmonella Pathogenicity Islands (SPI-1 to SPI-10) but also three novel SPIs (SPI-15, SPI-16, SPI-17) and other HGT events.</AbstractText><AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">The software is available under a GPL license as a standalone application at http://www.sanger.ac.uk/Software/analysis/alien_hunter</AbstractText><AbstractText Label="CONTACT" NlmCategory="BACKGROUND">gsv@sanger.ac.uk</AbstractText><AbstractText Label="SUPPLEMENTARY INFORMATION" NlmCategory="BACKGROUND">Supplementary data are available at Bioinformatics online.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Vernikos</LastName><ForeName>Georgios S</ForeName><Initials>GS</Initials><AffiliationInfo><Affiliation>The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SA, UK. gsv@sanger.ac.uk</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Parkhill</LastName><ForeName>Julian</ForeName><Initials>J</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><Agency>Wellcome Trust</Agency><Country>United Kingdom</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2006</Year><Month>07</Month><Day>12</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><ChemicalList><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D004269">DNA, Bacterial</NameOfSubstance></Chemical><Chemical><RegistryNumber>0</RegistryNumber><NameOfSubstance UI="D037521">Virulence Factors</NameOfSubstance></Chemical></ChemicalList><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="Y">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D005075" MajorTopicYN="N">Biological Evolution</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D004269" MajorTopicYN="N">DNA, Bacterial</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D022761" MajorTopicYN="N">Gene Transfer, Horizontal</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D016680" MajorTopicYN="N">Genome, Bacterial</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D044404" MajorTopicYN="N">Genomic Islands</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012475" MajorTopicYN="N">Salmonella</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName><QualifierName UI="Q000472" MajorTopicYN="Y">pathogenicity</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D014774" MajorTopicYN="N">Virulence</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="Y">genetics</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D037521" MajorTopicYN="N">Virulence Factors</DescriptorName><QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="pubmed"><Year>2006</Year><Month>7</Month><Day>14</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2006</Year><Month>9</Month><Day>26</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2006</Year><Month>7</Month><Day>14</Day><Hour>9</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">16837528</ArticleId><ArticleId IdType="pii">btl369</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btl369</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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