Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes
Identifieur interne : 002717 ( Istex/Corpus ); précédent : 002716; suivant : 002718Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes
Auteurs : Mateusz Janicki ; Rebecca Rooke ; Guojun YangSource :
- Chromosome Research [ 0967-3849 ] ; 2011-08-01.
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Abstract
Abstract: A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early computational analyses of TEs in genome sequences focused on filtering out “junk” sequences to facilitate gene annotation. When the high abundance and diversity of TEs in eukaryotic genomes were recognized, these early efforts transformed into the systematic genome-wide categorization and classification of TEs. The availability of genomic sequence data reversed the classical genetic approaches to discovering new TE families and superfamilies. Curated TE databases and their accurate annotation of genome sequences in turn facilitated the studies on TEs in a number of frontiers including: (1) TE-mediated changes of genome size and structure, (2) the influence of TEs on genome and gene functions, (3) TE regulation by host, (4) the evolution of TEs and their population dynamics, and (5) genomic scale studies of TE activity. Bioinformatics and genomic approaches have become an integral part of large-scale studies on TEs to extract information with pure in silico analyses or to assist wet lab experimental studies. The current revolution in genome sequencing technology facilitates further progress in the existing frontiers of research and emergence of new initiatives. The rapid generation of large-sequence datasets at record low costs on a routine basis is challenging the computing industry on storage capacity and manipulation speed and the bioinformatics community for improvement in algorithms and their implementations.
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DOI: 10.1007/s10577-011-9230-7
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<record><TEI wicri:istexFullTextTei="biblStruct"><teiHeader><fileDesc><titleStmt><title xml:lang="en">Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes</title><author><name sortKey="Janicki, Mateusz" sort="Janicki, Mateusz" uniqKey="Janicki M" first="Mateusz" last="Janicki">Mateusz Janicki</name><affiliation><mods:affiliation>Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6, Mississauga, ON, Canada</mods:affiliation></affiliation><affiliation><mods:affiliation>Cell and Systems Biology, University of Toronto, Toronto, Canada</mods:affiliation></affiliation></author><author><name sortKey="Rooke, Rebecca" sort="Rooke, Rebecca" uniqKey="Rooke R" first="Rebecca" last="Rooke">Rebecca Rooke</name><affiliation><mods:affiliation>Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6, Mississauga, ON, Canada</mods:affiliation></affiliation><affiliation><mods:affiliation>Cell and Systems Biology, University of Toronto, Toronto, Canada</mods:affiliation></affiliation></author><author><name sortKey="Yang, Guojun" sort="Yang, Guojun" uniqKey="Yang G" first="Guojun" last="Yang">Guojun Yang</name><affiliation><mods:affiliation>Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6, Mississauga, ON, Canada</mods:affiliation></affiliation><affiliation><mods:affiliation>Cell and Systems Biology, University of Toronto, Toronto, Canada</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: gage.yang@utoronto.ca</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:7EC2302966C5E7E3D32A76CEA6324D89580C6E5A</idno><date when="2011" year="2011">2011</date><idno type="doi">10.1007/s10577-011-9230-7</idno><idno type="url">https://api.istex.fr/ark:/67375/VQC-M8WBG8JQ-S/fulltext.pdf</idno><idno type="wicri:Area/Istex/Corpus">002717</idno><idno type="wicri:explorRef" wicri:stream="Istex" wicri:step="Corpus" wicri:corpus="ISTEX">002717</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes</title><author><name sortKey="Janicki, Mateusz" sort="Janicki, Mateusz" uniqKey="Janicki M" first="Mateusz" last="Janicki">Mateusz Janicki</name><affiliation><mods:affiliation>Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6, Mississauga, ON, Canada</mods:affiliation></affiliation><affiliation><mods:affiliation>Cell and Systems Biology, University of Toronto, Toronto, Canada</mods:affiliation></affiliation></author><author><name sortKey="Rooke, Rebecca" sort="Rooke, Rebecca" uniqKey="Rooke R" first="Rebecca" last="Rooke">Rebecca Rooke</name><affiliation><mods:affiliation>Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6, Mississauga, ON, Canada</mods:affiliation></affiliation><affiliation><mods:affiliation>Cell and Systems Biology, University of Toronto, Toronto, Canada</mods:affiliation></affiliation></author><author><name sortKey="Yang, Guojun" sort="Yang, Guojun" uniqKey="Yang G" first="Guojun" last="Yang">Guojun Yang</name><affiliation><mods:affiliation>Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6, Mississauga, ON, Canada</mods:affiliation></affiliation><affiliation><mods:affiliation>Cell and Systems Biology, University of Toronto, Toronto, Canada</mods:affiliation></affiliation><affiliation><mods:affiliation>E-mail: gage.yang@utoronto.ca</mods:affiliation></affiliation></author></analytic><monogr></monogr><series><title level="j">Chromosome Research</title><title level="j" type="sub">The Biology of Chromatin and Chromosomes</title><title level="j" type="abbrev">Chromosome Res</title><idno type="ISSN">0967-3849</idno><idno type="eISSN">1573-6849</idno><imprint><publisher>Springer Netherlands</publisher><pubPlace>Dordrecht</pubPlace><date type="published" when="2011-08-01">2011-08-01</date><biblScope unit="volume">19</biblScope><biblScope unit="issue">6</biblScope><biblScope unit="page" from="787">787</biblScope><biblScope unit="page" to="808">808</biblScope></imprint><idno type="ISSN">0967-3849</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0967-3849</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Bioinformatics</term><term>Genomics</term><term>Transposable Element</term><term>Transposon</term></keywords></textClass><langUsage><language ident="en">en</language></langUsage></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Abstract: A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early computational analyses of TEs in genome sequences focused on filtering out “junk” sequences to facilitate gene annotation. When the high abundance and diversity of TEs in eukaryotic genomes were recognized, these early efforts transformed into the systematic genome-wide categorization and classification of TEs. The availability of genomic sequence data reversed the classical genetic approaches to discovering new TE families and superfamilies. Curated TE databases and their accurate annotation of genome sequences in turn facilitated the studies on TEs in a number of frontiers including: (1) TE-mediated changes of genome size and structure, (2) the influence of TEs on genome and gene functions, (3) TE regulation by host, (4) the evolution of TEs and their population dynamics, and (5) genomic scale studies of TE activity. Bioinformatics and genomic approaches have become an integral part of large-scale studies on TEs to extract information with pure in silico analyses or to assist wet lab experimental studies. The current revolution in genome sequencing technology facilitates further progress in the existing frontiers of research and emergence of new initiatives. The rapid generation of large-sequence datasets at record low costs on a routine basis is challenging the computing industry on storage capacity and manipulation speed and the bioinformatics community for improvement in algorithms and their implementations.</div></front></TEI><istex><corpusName>springer-journals</corpusName><author><json:item><name>Mateusz Janicki</name><affiliations><json:string>Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6, Mississauga, ON, Canada</json:string><json:string>Cell and Systems Biology, University of Toronto, Toronto, Canada</json:string></affiliations></json:item><json:item><name>Rebecca Rooke</name><affiliations><json:string>Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6, Mississauga, ON, Canada</json:string><json:string>Cell and Systems Biology, University of Toronto, Toronto, Canada</json:string></affiliations></json:item><json:item><name>Guojun Yang</name><affiliations><json:string>Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6, Mississauga, ON, Canada</json:string><json:string>Cell and Systems Biology, University of Toronto, Toronto, Canada</json:string><json:string>E-mail: gage.yang@utoronto.ca</json:string></affiliations></json:item></author><subject><json:item><lang><json:string>eng</json:string></lang><value>Transposable Element</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Bioinformatics</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Genomics</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>Transposon</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>LINE : Long interspersed nuclear element</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>LTR : Long terminal repeat</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>MAK : MITE analysis toolkit</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>MITE : Miniature inverted repeat transposable element</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>MULE : Mutator-like element</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>SINE : Short interspersed nuclear element</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>TE : Transposable element</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>TESD : Transposable element simulator dynamics</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>TIR : Terminal inverted repeat</value></json:item><json:item><lang><json:string>eng</json:string></lang><value>TSD : Target site duplication</value></json:item></subject><articleId><json:string>9230</json:string><json:string>s10577-011-9230-7</json:string></articleId><arkIstex>ark:/67375/VQC-M8WBG8JQ-S</arkIstex><language><json:string>eng</json:string></language><originalGenre><json:string>OriginalPaper</json:string></originalGenre><abstract>Abstract: A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early computational analyses of TEs in genome sequences focused on filtering out “junk” sequences to facilitate gene annotation. When the high abundance and diversity of TEs in eukaryotic genomes were recognized, these early efforts transformed into the systematic genome-wide categorization and classification of TEs. The availability of genomic sequence data reversed the classical genetic approaches to discovering new TE families and superfamilies. Curated TE databases and their accurate annotation of genome sequences in turn facilitated the studies on TEs in a number of frontiers including: (1) TE-mediated changes of genome size and structure, (2) the influence of TEs on genome and gene functions, (3) TE regulation by host, (4) the evolution of TEs and their population dynamics, and (5) genomic scale studies of TE activity. Bioinformatics and genomic approaches have become an integral part of large-scale studies on TEs to extract information with pure in silico analyses or to assist wet lab experimental studies. The current revolution in genome sequencing technology facilitates further progress in the existing frontiers of research and emergence of new initiatives. 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ident="en">en</language></langUsage><abstract xml:lang="en"><p>Abstract: A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early computational analyses of TEs in genome sequences focused on filtering out “junk” sequences to facilitate gene annotation. When the high abundance and diversity of TEs in eukaryotic genomes were recognized, these early efforts transformed into the systematic genome-wide categorization and classification of TEs. The availability of genomic sequence data reversed the classical genetic approaches to discovering new TE families and superfamilies. Curated TE databases and their accurate annotation of genome sequences in turn facilitated the studies on TEs in a number of frontiers including: (1) TE-mediated changes of genome size and structure, (2) the influence of TEs on genome and gene functions, (3) TE regulation by host, (4) the evolution of TEs and their population dynamics, and (5) genomic scale studies of TE activity. Bioinformatics and genomic approaches have become an integral part of large-scale studies on TEs to extract information with pure in silico analyses or to assist wet lab experimental studies. The current revolution in genome sequencing technology facilitates further progress in the existing frontiers of research and emergence of new initiatives. The rapid generation of large-sequence datasets at record low costs on a routine basis is challenging the computing industry on storage capacity and manipulation speed and the bioinformatics community for improvement in algorithms and their implementations.</p></abstract><textClass xml:lang="en"><keywords scheme="keyword"><list><head>Keywords</head><item><term>Transposable Element</term></item><item><term>Bioinformatics</term></item><item><term>Genomics</term></item><item><term>Transposon</term></item></list></keywords></textClass><textClass><keywords scheme="keyword"><list><head>Abbreviations</head><item><term>LINE</term><term>Long interspersed nuclear element</term></item><item><term>LTR</term><term>Long terminal repeat</term></item><item><term>MAK</term><term>MITE analysis toolkit</term></item><item><term>MITE</term><term>Miniature inverted repeat transposable element</term></item><item><term>MULE</term><term>Mutator-like element</term></item><item><term>SINE</term><term>Short interspersed nuclear element</term></item><item><term>TE</term><term>Transposable element</term></item><item><term>TESD</term><term>Transposable element simulator dynamics</term></item><item><term>TIR</term><term>Terminal inverted repeat</term></item><item><term>TSD</term><term>Target site duplication</term></item></list></keywords></textClass><textClass><keywords scheme="Journal Subject"><list><head>Life Sciences</head><item><term>Cell Biology</term></item><item><term>Plant Genetics & Genomics</term></item><item><term>Animal Genetics and Genomics</term></item><item><term>Human Genetics</term></item></list></keywords></textClass></profileDesc><revisionDesc><change when="2011-08-01">Published</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><extension>txt</extension><original>false</original><mimetype>text/plain</mimetype><uri>https://api.istex.fr/ark:/67375/VQC-M8WBG8JQ-S/fulltext.txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="corpus springer-journals not found" wicri:toSee="no header"><istex:xmlDeclaration>version="1.0" encoding="UTF-8"</istex:xmlDeclaration><istex:docType PUBLIC="-//Springer-Verlag//DTD A++ V2.4//EN" URI="http://devel.springer.de/A++/V2.4/DTD/A++V2.4.dtd" name="istex:docType"></istex:docType><istex:document><Publisher><PublisherInfo><PublisherName>Springer Netherlands</PublisherName><PublisherLocation>Dordrecht</PublisherLocation></PublisherInfo><Journal OutputMedium="All"><JournalInfo JournalProductType="NonStandardArchiveJournal" NumberingStyle="Unnumbered"><JournalID>10577</JournalID><JournalPrintISSN>0967-3849</JournalPrintISSN><JournalElectronicISSN>1573-6849</JournalElectronicISSN><JournalTitle>Chromosome Research</JournalTitle><JournalSubTitle>The Biology of Chromatin and Chromosomes</JournalSubTitle><JournalAbbreviatedTitle>Chromosome Res</JournalAbbreviatedTitle><JournalSubjectGroup><JournalSubject Type="Primary">Life Sciences</JournalSubject><JournalSubject Type="Secondary">Cell Biology</JournalSubject><JournalSubject Type="Secondary">Plant Genetics & Genomics</JournalSubject><JournalSubject Type="Secondary">Animal Genetics and Genomics</JournalSubject><JournalSubject Type="Secondary">Human Genetics</JournalSubject></JournalSubjectGroup></JournalInfo><Volume OutputMedium="All"><VolumeInfo TocLevels="0" VolumeType="Regular"><VolumeIDStart>19</VolumeIDStart><VolumeIDEnd>19</VolumeIDEnd><VolumeIssueCount>8</VolumeIssueCount></VolumeInfo><Issue IssueType="Regular" OutputMedium="All"><IssueInfo IssueType="Regular" TocLevels="0"><IssueIDStart>6</IssueIDStart><IssueIDEnd>6</IssueIDEnd><IssueArticleCount>10</IssueArticleCount><IssueHistory><OnlineDate><Year>2011</Year><Month>10</Month><Day>5</Day></OnlineDate><PrintDate><Year>2011</Year><Month>10</Month><Day>4</Day></PrintDate><CoverDate><Year>2011</Year><Month>8</Month></CoverDate><PricelistYear>2011</PricelistYear></IssueHistory><IssueCopyright><CopyrightHolderName>Springer Science+Business Media B.V.</CopyrightHolderName><CopyrightYear>2011</CopyrightYear></IssueCopyright></IssueInfo><Article ID="s10577-011-9230-7" OutputMedium="All"><ArticleInfo ArticleType="OriginalPaper" ContainsESM="No" Language="En" NumberingStyle="Unnumbered" TocLevels="0"><ArticleID>9230</ArticleID><ArticleDOI>10.1007/s10577-011-9230-7</ArticleDOI><ArticleCitationID>787</ArticleCitationID><ArticleSequenceNumber>8</ArticleSequenceNumber><ArticleTitle Language="En">Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes</ArticleTitle><ArticleFirstPage>787</ArticleFirstPage><ArticleLastPage>808</ArticleLastPage><ArticleHistory><RegistrationDate><Year>2011</Year><Month>8</Month><Day>5</Day></RegistrationDate><OnlineDate><Year>2011</Year><Month>8</Month><Day>18</Day></OnlineDate></ArticleHistory><ArticleEditorialResponsibility>T. Ryan Gregory and Jillian D. Bainard</ArticleEditorialResponsibility><ArticleCopyright><CopyrightHolderName>Springer Science+Business Media B.V.</CopyrightHolderName><CopyrightYear>2011</CopyrightYear></ArticleCopyright><ArticleGrants 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></ArticleGrants></ArticleInfo><ArticleHeader><AuthorGroup><Author AffiliationIDS="Aff1 Aff2"><AuthorName DisplayOrder="Western"><GivenName>Mateusz</GivenName><FamilyName>Janicki</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff1 Aff2"><AuthorName DisplayOrder="Western"><GivenName>Rebecca</GivenName><FamilyName>Rooke</FamilyName></AuthorName></Author><Author AffiliationIDS="Aff1 Aff2" CorrespondingAffiliationID="Aff1"><AuthorName DisplayOrder="Western"><GivenName>Guojun</GivenName><FamilyName>Yang</FamilyName></AuthorName><Contact><Phone>+1-905-5694751</Phone><Fax>+1-905-8283792</Fax><Email>gage.yang@utoronto.ca</Email></Contact></Author><Affiliation ID="Aff1"><OrgDivision>Department of Biology</OrgDivision><OrgName>University of Toronto at Mississauga</OrgName><OrgAddress><Street>3359 Mississauga Road</Street><City>Mississauga</City><State>ON</State><Postcode>L5L 1C6</Postcode><Country Code="CA">Canada</Country></OrgAddress></Affiliation><Affiliation ID="Aff2"><OrgDivision>Cell and Systems Biology</OrgDivision><OrgName>University of Toronto</OrgName><OrgAddress><City>Toronto</City><Country Code="CA">Canada</Country></OrgAddress></Affiliation></AuthorGroup><Abstract ID="Abs1" Language="En" OutputMedium="All"><Heading>Abstract</Heading><Para TextBreak="No">A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early computational analyses of TEs in genome sequences focused on filtering out “junk” sequences to facilitate gene annotation. When the high abundance and diversity of TEs in eukaryotic genomes were recognized, these early efforts transformed into the systematic genome-wide categorization and classification of TEs. The availability of genomic sequence data reversed the classical genetic approaches to discovering new TE families and superfamilies. Curated TE databases and their accurate annotation of genome sequences in turn facilitated the studies on TEs in a number of frontiers including: (1) TE-mediated changes of genome size and structure, (2) the influence of TEs on genome and gene functions, (3) TE regulation by host, (4) the evolution of TEs and their population dynamics, and (5) genomic scale studies of TE activity. Bioinformatics and genomic approaches have become an integral part of large-scale studies on TEs to extract information with pure in silico analyses or to assist wet lab experimental studies. The current revolution in genome sequencing technology facilitates further progress in the existing frontiers of research and emergence of new initiatives. The rapid generation of large-sequence datasets at record low costs on a routine basis is challenging the computing industry on storage capacity and manipulation speed and the bioinformatics community for improvement in algorithms and their implementations.</Para></Abstract><KeywordGroup Language="En" OutputMedium="All"><Heading>Keywords</Heading><Keyword>Transposable Element</Keyword><Keyword>Bioinformatics</Keyword><Keyword>Genomics</Keyword><Keyword>Transposon</Keyword></KeywordGroup><AbbreviationGroup><Heading>Abbreviations</Heading><DefinitionList><DefinitionListEntry><Term>LINE</Term><Description><Para TextBreak="No">Long interspersed nuclear element</Para></Description></DefinitionListEntry><DefinitionListEntry><Term>LTR</Term><Description><Para TextBreak="No">Long terminal repeat</Para></Description></DefinitionListEntry><DefinitionListEntry><Term>MAK</Term><Description><Para TextBreak="No">MITE analysis toolkit</Para></Description></DefinitionListEntry><DefinitionListEntry><Term>MITE</Term><Description><Para TextBreak="No">Miniature inverted repeat transposable element</Para></Description></DefinitionListEntry><DefinitionListEntry><Term>MULE</Term><Description><Para TextBreak="No"><Emphasis Type="Italic">Mutator</Emphasis>-like element</Para></Description></DefinitionListEntry><DefinitionListEntry><Term>SINE</Term><Description><Para TextBreak="No">Short interspersed nuclear element</Para></Description></DefinitionListEntry><DefinitionListEntry><Term>TE</Term><Description><Para TextBreak="No">Transposable element</Para></Description></DefinitionListEntry><DefinitionListEntry><Term>TESD</Term><Description><Para TextBreak="No">Transposable element simulator dynamics</Para></Description></DefinitionListEntry><DefinitionListEntry><Term>TIR</Term><Description><Para TextBreak="No">Terminal inverted repeat</Para></Description></DefinitionListEntry><DefinitionListEntry><Term>TSD</Term><Description><Para TextBreak="No">Target site duplication</Para></Description></DefinitionListEntry></DefinitionList></AbbreviationGroup><ArticleNote Type="CommunicatedBy"><SimplePara>Responsible Editor: T. Ryan Gregory and Jillian D. Bainard.</SimplePara></ArticleNote></ArticleHeader><NoBody></NoBody></Article></Issue></Volume></Journal></Publisher></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes</title></titleInfo><titleInfo type="alternative" contentType="CDATA"><title>Bioinformatics and genomic analysis of transposable elements in eukaryotic genomes</title></titleInfo><name type="personal"><namePart type="given">Mateusz</namePart><namePart type="family">Janicki</namePart><affiliation>Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6, Mississauga, ON, Canada</affiliation><affiliation>Cell and Systems Biology, University of Toronto, Toronto, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Rebecca</namePart><namePart type="family">Rooke</namePart><affiliation>Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6, Mississauga, ON, Canada</affiliation><affiliation>Cell and Systems Biology, University of Toronto, Toronto, Canada</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal" displayLabel="corresp"><namePart type="given">Guojun</namePart><namePart type="family">Yang</namePart><affiliation>Department of Biology, University of Toronto at Mississauga, 3359 Mississauga Road, L5L 1C6, Mississauga, ON, Canada</affiliation><affiliation>Cell and Systems Biology, University of Toronto, Toronto, Canada</affiliation><affiliation>E-mail: gage.yang@utoronto.ca</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="research-article" displayLabel="OriginalPaper" authority="ISTEX" authorityURI="https://content-type.data.istex.fr" valueURI="https://content-type.data.istex.fr/ark:/67375/XTP-1JC4F85T-7">research-article</genre><originInfo><publisher>Springer Netherlands</publisher><place><placeTerm type="text">Dordrecht</placeTerm></place><dateIssued encoding="w3cdtf">2011-08-01</dateIssued><copyrightDate encoding="w3cdtf">2011</copyrightDate></originInfo><language><languageTerm type="code" authority="rfc3066">en</languageTerm><languageTerm type="code" authority="iso639-2b">eng</languageTerm></language><abstract lang="en">Abstract: A major portion of most eukaryotic genomes are transposable elements (TEs). During evolution, TEs have introduced profound changes to genome size, structure, and function. As integral parts of genomes, the dynamic presence of TEs will continue to be a major force in reshaping genomes. Early computational analyses of TEs in genome sequences focused on filtering out “junk” sequences to facilitate gene annotation. When the high abundance and diversity of TEs in eukaryotic genomes were recognized, these early efforts transformed into the systematic genome-wide categorization and classification of TEs. The availability of genomic sequence data reversed the classical genetic approaches to discovering new TE families and superfamilies. Curated TE databases and their accurate annotation of genome sequences in turn facilitated the studies on TEs in a number of frontiers including: (1) TE-mediated changes of genome size and structure, (2) the influence of TEs on genome and gene functions, (3) TE regulation by host, (4) the evolution of TEs and their population dynamics, and (5) genomic scale studies of TE activity. Bioinformatics and genomic approaches have become an integral part of large-scale studies on TEs to extract information with pure in silico analyses or to assist wet lab experimental studies. The current revolution in genome sequencing technology facilitates further progress in the existing frontiers of research and emergence of new initiatives. The rapid generation of large-sequence datasets at record low costs on a routine basis is challenging the computing industry on storage capacity and manipulation speed and the bioinformatics community for improvement in algorithms and their implementations.</abstract><subject lang="en"><genre>Keywords</genre><topic>Transposable Element</topic><topic>Bioinformatics</topic><topic>Genomics</topic><topic>Transposon</topic></subject><subject><genre>Abbreviations</genre><topic>LINE : Long interspersed nuclear element</topic><topic>LTR : Long terminal repeat</topic><topic>MAK : MITE analysis toolkit</topic><topic>MITE : Miniature inverted repeat transposable element</topic><topic>MULE : Mutator-like element</topic><topic>SINE : Short interspersed nuclear element</topic><topic>TE : Transposable element</topic><topic>TESD : Transposable element simulator dynamics</topic><topic>TIR : Terminal inverted repeat</topic><topic>TSD : Target site duplication</topic></subject><relatedItem type="host"><titleInfo><title>Chromosome Research</title><subTitle>The Biology of Chromatin and Chromosomes</subTitle></titleInfo><titleInfo type="abbreviated"><title>Chromosome Res</title></titleInfo><genre type="journal" authority="ISTEX" authorityURI="https://publication-type.data.istex.fr" valueURI="https://publication-type.data.istex.fr/ark:/67375/JMC-0GLKJH51-B">journal</genre><originInfo><publisher>Springer</publisher><dateIssued encoding="w3cdtf">2011-10-05</dateIssued><copyrightDate encoding="w3cdtf">2011</copyrightDate></originInfo><subject><genre>Life Sciences</genre><topic>Cell Biology</topic><topic>Plant Genetics & Genomics</topic><topic>Animal Genetics and Genomics</topic><topic>Human Genetics</topic></subject><identifier type="ISSN">0967-3849</identifier><identifier type="eISSN">1573-6849</identifier><identifier type="JournalID">10577</identifier><identifier type="IssueArticleCount">10</identifier><identifier type="VolumeIssueCount">8</identifier><part><date>2011</date><detail type="volume"><number>19</number><caption>vol.</caption></detail><detail type="issue"><number>6</number><caption>no.</caption></detail><extent unit="pages"><start>787</start><end>808</end></extent></part><recordInfo><recordOrigin>Springer Science+Business Media B.V., 2011</recordOrigin></recordInfo></relatedItem><identifier type="istex">7EC2302966C5E7E3D32A76CEA6324D89580C6E5A</identifier><identifier type="ark">ark:/67375/VQC-M8WBG8JQ-S</identifier><identifier type="DOI">10.1007/s10577-011-9230-7</identifier><identifier type="ArticleID">9230</identifier><identifier type="ArticleID">s10577-011-9230-7</identifier><accessCondition type="use and reproduction" contentType="copyright">Springer Science+Business Media B.V., 2011</accessCondition><recordInfo><recordContentSource authority="ISTEX" authorityURI="https://loaded-corpus.data.istex.fr" valueURI="https://loaded-corpus.data.istex.fr/ark:/67375/XBH-3XSW68JL-F">springer</recordContentSource><recordOrigin>Springer Science+Business Media B.V., 2011</recordOrigin></recordInfo></mods><json:item><extension>json</extension><original>false</original><mimetype>application/json</mimetype><uri>https://api.istex.fr/ark:/67375/VQC-M8WBG8JQ-S/record.json</uri></json:item></metadata><serie></serie></istex></record>Pour manipuler ce document sous Unix (Dilib)
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