TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis
Identifieur interne : 000179 ( Istex/Corpus ); précédent : 000178; suivant : 000180TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis
Auteurs : Stein Aerts ; Peter Van Loo ; Gert Thijs ; Herbert Mayer ; Rainer De Martin ; Yves Moreau ; Bart De MoorSource :
- Nucleic Acids Research [ 0305-1048 ] ; 2005-07-01.
Abstract
We present the second and improved release of the TOUCAN workbench for cis-regulatory sequence analysis. TOUCAN implements and integrates fast state-of-the-art methods and strategies in gene regulation bioinformatics, including algorithms for comparative genomics and for the detection of cis-regulatory modules. This second release of TOUCAN has become open source and thereby carries the potential to evolve rapidly. The main goal of TOUCAN is to allow a user to come to testable hypotheses regarding the regulation of a gene or of a set of co-regulated genes. TOUCAN can be launched from this location: http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php.
Url:
DOI: 10.1093/nar/gki354
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Tel: +32 16 347150; Fax: +32 16 346218; Email: stein.aerts@med.kuleuven.ac.be</mods:affiliation></affiliation></author><author><name sortKey="Van Loo, Peter" sort="Van Loo, Peter" uniqKey="Van Loo P" first="Peter" last="Van Loo">Peter Van Loo</name><affiliation><mods:affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</mods:affiliation></affiliation><affiliation><mods:affiliation>Human Genome Laboratory, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and K.U.Leuven Belgium</mods:affiliation></affiliation></author><author><name sortKey="Thijs, Gert" sort="Thijs, Gert" uniqKey="Thijs G" first="Gert" last="Thijs">Gert Thijs</name><affiliation><mods:affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</mods:affiliation></affiliation></author><author><name sortKey="Mayer, Herbert" sort="Mayer, Herbert" uniqKey="Mayer H" first="Herbert" last="Mayer">Herbert Mayer</name><affiliation><mods:affiliation>Center for Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University Vienna, and Biomolecular Therapeutics Vienna, Austria</mods:affiliation></affiliation></author><author><name sortKey="De Martin, Rainer" sort="De Martin, Rainer" uniqKey="De Martin R" first="Rainer" last="De Martin">Rainer De Martin</name><affiliation><mods:affiliation>Center for Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University Vienna, and Biomolecular Therapeutics Vienna, Austria</mods:affiliation></affiliation></author><author><name sortKey="Moreau, Yves" sort="Moreau, Yves" uniqKey="Moreau Y" first="Yves" last="Moreau">Yves Moreau</name><affiliation><mods:affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</mods:affiliation></affiliation></author><author><name sortKey="De Moor, Bart" sort="De Moor, Bart" uniqKey="De Moor B" first="Bart" last="De Moor">Bart De Moor</name><affiliation><mods:affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</mods:affiliation></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">ISTEX</idno><idno type="RBID">ISTEX:8753078D78532410122AB9170AE54357411F1010</idno><date when="2005" year="2005">2005</date><idno type="doi">10.1093/nar/gki354</idno><idno type="url">https://api.istex.fr/document/8753078D78532410122AB9170AE54357411F1010/fulltext/pdf</idno><idno type="wicri:Area/Istex/Corpus">000179</idno></publicationStmt><sourceDesc><biblStruct><analytic><title level="a" type="main" xml:lang="en">TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis</title><author><name sortKey="Aerts, Stein" sort="Aerts, Stein" uniqKey="Aerts S" first="Stein" last="Aerts">Stein Aerts</name><affiliation><mods:affiliation>Laboratory of Neurogenetics, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and K.U.Leuven Belgium</mods:affiliation></affiliation><affiliation><mods:affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</mods:affiliation></affiliation><affiliation><mods:affiliation>To whom correspondence should be addressed at Laboratory of Neurogenetics, Department of Human Genetics, Herestraat 49 bus 602, 3000 Leuven, Belgium. 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TOUCAN implements and integrates fast state-of-the-art methods and strategies in gene regulation bioinformatics, including algorithms for comparative genomics and for the detection of cis-regulatory modules. This second release of TOUCAN has become open source and thereby carries the potential to evolve rapidly. The main goal of TOUCAN is to allow a user to come to testable hypotheses regarding the regulation of a gene or of a set of co-regulated genes. 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Tel: +32 16 347150; Fax: +32 16 346218; Email: stein.aerts@med.kuleuven.ac.be</json:string><json:string>E-mail: stein.aerts@med.kuleuven.ac.be</json:string></affiliations></json:item><json:item><name>Peter Van Loo</name><affiliations><json:string>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</json:string><json:string>Human Genome Laboratory, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and K.U.Leuven Belgium</json:string></affiliations></json:item><json:item><name>Gert Thijs</name><affiliations><json:string>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</json:string></affiliations></json:item><json:item><name>Herbert Mayer</name><affiliations><json:string>Center for Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University Vienna, and Biomolecular Therapeutics Vienna, Austria</json:string></affiliations></json:item><json:item><name>Rainer de Martin</name><affiliations><json:string>Center for Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University Vienna, and Biomolecular Therapeutics Vienna, Austria</json:string></affiliations></json:item><json:item><name>Yves Moreau</name><affiliations><json:string>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</json:string></affiliations></json:item><json:item><name>Bart De Moor</name><affiliations><json:string>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</json:string></affiliations></json:item></author><language><json:string>eng</json:string></language><originalGenre><json:string>other</json:string></originalGenre><abstract>We present the second and improved release of the TOUCAN workbench for cis-regulatory sequence analysis. 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Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oupjournals.org</p></availability><date>2005</date></publicationStmt><notesStmt><note>*To whom correspondence should be addressed at Laboratory of Neurogenetics, Department of Human Genetics, Herestraat 49 bus 602, 3000 Leuven, Belgium. Tel: +32 16 347150; Fax: +32 16 346218; Email: stein.aerts@med.kuleuven.ac.be</note></notesStmt><sourceDesc><biblStruct type="inbook"><analytic><title level="a" type="main" xml:lang="en">TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis</title><author xml:id="author-1"><persName><forename type="first">Stein</forename><surname>Aerts</surname></persName><affiliation>Laboratory of Neurogenetics, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and K.U.Leuven Belgium</affiliation><affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</affiliation><affiliation>To whom correspondence should be addressed at Laboratory of Neurogenetics, Department of Human Genetics, Herestraat 49 bus 602, 3000 Leuven, Belgium. Tel: +32 16 347150; Fax: +32 16 346218; Email: stein.aerts@med.kuleuven.ac.be</affiliation></author><author xml:id="author-2"><persName><forename type="first">Peter</forename><surname>Van Loo</surname></persName><affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</affiliation><affiliation>Human Genome Laboratory, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and K.U.Leuven Belgium</affiliation></author><author xml:id="author-3"><persName><forename type="first">Gert</forename><surname>Thijs</surname></persName><affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</affiliation></author><author xml:id="author-4"><persName><forename type="first">Herbert</forename><surname>Mayer</surname></persName><affiliation>Center for Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University Vienna, and Biomolecular Therapeutics Vienna, Austria</affiliation></author><author xml:id="author-5"><persName><forename type="first">Rainer</forename><surname>de Martin</surname></persName><affiliation>Center for Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University Vienna, and Biomolecular Therapeutics Vienna, Austria</affiliation></author><author xml:id="author-6"><persName><forename type="first">Yves</forename><surname>Moreau</surname></persName><affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</affiliation></author><author xml:id="author-7"><persName><forename type="first">Bart</forename><surname>De Moor</surname></persName><affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</affiliation></author></analytic><monogr><title level="j">Nucleic Acids Research</title><title level="j" type="abbrev">Nucl. Acids Res.</title><idno type="pISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published" when="2005-07-01"></date><biblScope unit="volume">33</biblScope><biblScope unit="supplement">suppl_2</biblScope><biblScope unit="page" from="W393">W393</biblScope><biblScope unit="page" to="W396">W396</biblScope></imprint></monogr><idno type="istex">8753078D78532410122AB9170AE54357411F1010</idno><idno type="DOI">10.1093/nar/gki354</idno><idno type="local">gki354</idno></biblStruct></sourceDesc></fileDesc><profileDesc><creation><date>2005</date></creation><langUsage><language ident="en">en</language></langUsage><abstract xml:lang="en"><p>We present the second and improved release of the TOUCAN workbench for cis-regulatory sequence analysis. TOUCAN implements and integrates fast state-of-the-art methods and strategies in gene regulation bioinformatics, including algorithms for comparative genomics and for the detection of cis-regulatory modules. This second release of TOUCAN has become open source and thereby carries the potential to evolve rapidly. The main goal of TOUCAN is to allow a user to come to testable hypotheses regarding the regulation of a gene or of a set of co-regulated genes. TOUCAN can be launched from this location: http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php.</p></abstract></profileDesc><revisionDesc><change when="2005-07-01">Published</change><change xml:id="refBibs-istex" who="#ISTEX-API" when="2016-10-14">References added</change></revisionDesc></teiHeader></istex:fulltextTEI><json:item><original>false</original><mimetype>text/plain</mimetype><extension>txt</extension><uri>https://api.istex.fr/document/8753078D78532410122AB9170AE54357411F1010/fulltext/txt</uri></json:item></fulltext><metadata><istex:metadataXml wicri:clean="corpus oup" wicri:toSee="no header"><istex:xmlDeclaration>version="1.0" encoding="US-ASCII"</istex:xmlDeclaration><istex:docType PUBLIC="-//NLM//DTD Journal Publishing DTD v2.3 20070202//EN" URI="journalpublishing.dtd" name="istex:docType"></istex:docType><istex:document><article xml:lang="en" article-type="other"><front><journal-meta><journal-id journal-id-type="hwp">nar</journal-id><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-title>Nucleic Acids Research</journal-title><abbrev-journal-title abbrev-type="publisher">Nucl. Acids Res.</abbrev-journal-title><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="other">gki354</article-id><article-id pub-id-type="doi">10.1093/nar/gki354</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Aerts</surname><given-names>Stein</given-names></name><xref rid="AU1">1</xref><xref rid="AU2">2</xref><xref rid="COR1">*</xref></contrib><contrib contrib-type="author"><name><surname>Van Loo</surname><given-names>Peter</given-names></name><xref rid="AU2">2</xref><xref rid="AU3">3</xref></contrib><contrib contrib-type="author"><name><surname>Thijs</surname><given-names>Gert</given-names></name><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>Mayer</surname><given-names>Herbert</given-names></name><xref rid="AU4">4</xref></contrib><contrib contrib-type="author"><name><surname>de Martin</surname><given-names>Rainer</given-names></name><xref rid="AU4">4</xref></contrib><contrib contrib-type="author"><name><surname>Moreau</surname><given-names>Yves</given-names></name><xref rid="AU2">2</xref></contrib><contrib contrib-type="author"><name><surname>De Moor</surname><given-names>Bart</given-names></name><xref rid="AU2">2</xref></contrib><aff id="AU1"><sup>1</sup>Laboratory of Neurogenetics, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and K.U.Leuven Belgium</aff><aff id="AU2"><sup>2</sup>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</aff><aff id="AU3"><sup>3</sup>Human Genome Laboratory, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and K.U.Leuven Belgium</aff><aff id="AU4"><sup>4</sup>Center for Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University Vienna, and Biomolecular Therapeutics Vienna, Austria</aff></contrib-group><author-notes><corresp id="COR1"><sup>*</sup>To whom correspondence should be addressed at Laboratory of Neurogenetics, Department of Human Genetics, Herestraat 49 bus 602, 3000 Leuven, Belgium. Tel: +32 16 347150; Fax: +32 16 346218; Email: <ext-link xlink:href="stein.aerts@med.kuleuven.ac.be" ext-link-type="email">stein.aerts@med.kuleuven.ac.be</ext-link></corresp></author-notes><pub-date pub-type="ppub"><day>1</day><month>7</month><year>2005</year></pub-date><volume>33</volume><issue>suppl_2</issue><fpage>W393</fpage><lpage>W396</lpage><history><date date-type="accepted"><day>7</day><month>1</month><year>2005</year></date><date date-type="received"><day>12</day><month>11</month><year>2004</year></date><date date-type="rev-recd"><day>15</day><month>12</month><year>2004</year></date></history><permissions><copyright-statement>© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact <ext-link xlink:href="journals.permissions@oupjournals.org" ext-link-type="email">journals.permissions@oupjournals.org</ext-link></copyright-statement><copyright-year>2005</copyright-year><license license-type="open-access"><p></p></license></permissions><abstract xml:lang="en"><p>We present the second and improved release of the TOUCAN workbench for <italic>cis</italic>-regulatory sequence analysis. TOUCAN implements and integrates fast state-of-the-art methods and strategies in gene regulation bioinformatics, including algorithms for comparative genomics and for the detection of <italic>cis</italic>-regulatory modules. This second release of TOUCAN has become open source and thereby carries the potential to evolve rapidly. The main goal of TOUCAN is to allow a user to come to testable hypotheses regarding the regulation of a gene or of a set of co-regulated genes. TOUCAN can be launched from this location: <ext-link xlink:href="http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php" ext-link-type="url">http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php</ext-link>.</p></abstract><custom-meta-wrap><custom-meta><meta-name>hwp-legacy-fpage</meta-name><meta-value>W393</meta-value></custom-meta><custom-meta><meta-name>cover-date</meta-name><meta-value></meta-value></custom-meta><custom-meta><meta-name>hwp-legacy-dochead</meta-name><meta-value>research-article</meta-value></custom-meta></custom-meta-wrap></article-meta></front></article></istex:document></istex:metadataXml><mods version="3.6"><titleInfo lang="en"><title>TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis</title></titleInfo><titleInfo type="alternative" lang="en" contentType="CDATA"><title>TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis</title></titleInfo><name type="personal"><namePart type="given">Stein</namePart><namePart type="family">Aerts</namePart><affiliation>Laboratory of Neurogenetics, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and K.U.Leuven Belgium</affiliation><affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</affiliation><affiliation>To whom correspondence should be addressed at Laboratory of Neurogenetics, Department of Human Genetics, Herestraat 49 bus 602, 3000 Leuven, Belgium. Tel: +32 16 347150; Fax: +32 16 346218; Email: stein.aerts@med.kuleuven.ac.be</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Peter</namePart><namePart type="family">Van Loo</namePart><affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</affiliation><affiliation>Human Genome Laboratory, Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology and K.U.Leuven Belgium</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Gert</namePart><namePart type="family">Thijs</namePart><affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Herbert</namePart><namePart type="family">Mayer</namePart><affiliation>Center for Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University Vienna, and Biomolecular Therapeutics Vienna, Austria</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Rainer</namePart><namePart type="family">de Martin</namePart><affiliation>Center for Biomolecular Medicine and Pharmacology, Department of Vascular Biology and Thrombosis Research, Medical University Vienna, and Biomolecular Therapeutics Vienna, Austria</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Yves</namePart><namePart type="family">Moreau</namePart><affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</affiliation><role><roleTerm type="text">author</roleTerm></role></name><name type="personal"><namePart type="given">Bart</namePart><namePart type="family">De Moor</namePart><affiliation>Bioinformatics group, Department of Electrical Engineering ESAT-SCD, K.U.Leuven Belgium</affiliation><role><roleTerm type="text">author</roleTerm></role></name><typeOfResource>text</typeOfResource><genre type="other" displayLabel="other"></genre><originInfo><publisher>Oxford University Press</publisher><dateIssued encoding="w3cdtf">2005-07-01</dateIssued><copyrightDate encoding="w3cdtf">2005</copyrightDate></originInfo><language><languageTerm type="code" authority="iso639-2b">eng</languageTerm><languageTerm type="code" authority="rfc3066">en</languageTerm></language><physicalDescription><internetMediaType>text/html</internetMediaType></physicalDescription><abstract lang="en">We present the second and improved release of the TOUCAN workbench for cis-regulatory sequence analysis. TOUCAN implements and integrates fast state-of-the-art methods and strategies in gene regulation bioinformatics, including algorithms for comparative genomics and for the detection of cis-regulatory modules. This second release of TOUCAN has become open source and thereby carries the potential to evolve rapidly. The main goal of TOUCAN is to allow a user to come to testable hypotheses regarding the regulation of a gene or of a set of co-regulated genes. TOUCAN can be launched from this location: http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php.</abstract><note type="author-notes">*To whom correspondence should be addressed at Laboratory of Neurogenetics, Department of Human Genetics, Herestraat 49 bus 602, 3000 Leuven, Belgium. Tel: +32 16 347150; Fax: +32 16 346218; Email: stein.aerts@med.kuleuven.ac.be</note><relatedItem type="host"><titleInfo><title>Nucleic Acids Research</title></titleInfo><titleInfo type="abbreviated"><title>Nucl. Acids Res.</title></titleInfo><genre type="journal">journal</genre><identifier type="ISSN">0305-1048</identifier><identifier type="eISSN">1362-4962</identifier><identifier type="PublisherID">nar</identifier><identifier type="PublisherID-hwp">nar</identifier><identifier type="PublisherID-nlm-ta">Nucleic Acids Res</identifier><part><date>2005</date><detail type="volume"><caption>vol.</caption><number>33</number></detail><detail type="supplement"><number>suppl_2</number></detail><extent unit="pages"><start>W393</start><end>W396</end></extent></part></relatedItem><identifier type="istex">8753078D78532410122AB9170AE54357411F1010</identifier><identifier type="DOI">10.1093/nar/gki354</identifier><identifier type="local">gki354</identifier><accessCondition type="use and reproduction" contentType="copyright">© The Author 2005. Published by Oxford University Press. All rights reserved
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