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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">CysView: protein classification based on cysteine pairing patterns</title><author><name sortKey="Lenffer, Johann" sort="Lenffer, Johann" uniqKey="Lenffer J" first="Johann" last="Lenffer">Johann Lenffer</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">School of Molecular and Microbial Biosciences, Building G08, University of Sydney, NSW 2006, Australia,</nlm:aff></affiliation></author><author><name sortKey="Lai, Paulo" sort="Lai, Paulo" uniqKey="Lai P" first="Paulo" last="Lai">Paulo Lai</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">School of Molecular and Microbial Biosciences, Building G08, University of Sydney, NSW 2006, Australia,</nlm:aff></affiliation></author><author><name sortKey="El Mejaber, Wafaa" sort="El Mejaber, Wafaa" uniqKey="El Mejaber W" first="Wafaa" last="El Mejaber">Wafaa El Mejaber</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="N0x8b519a0.0x9b2ac08">IUP Génie Physiologique et Informatique, Bâtiment botanique, 40 av. Recteur Pineau-86022, Poitiers Cedex, France</nlm:aff></affiliation></author><author><name sortKey="Khan, Asif M" sort="Khan, Asif M" uniqKey="Khan A" first="Asif M." last="Khan">Asif M. Khan</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="N0x8b519a0.0x9b2ac08">Department of Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Koh, Judice L Y" sort="Koh, Judice L Y" uniqKey="Koh J" first="Judice L. Y." last="Koh">Judice L. Y. Koh</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation></author><author><name sortKey="Tan, Paul T J" sort="Tan, Paul T J" uniqKey="Tan P" first="Paul T. J." last="Tan">Paul T. J. Tan</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="N0x8b519a0.0x9b2ac08">Department of Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Seah, Seng H" sort="Seah, Seng H" uniqKey="Seah S" first="Seng H." last="Seah">Seng H. Seah</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation></author><author><name sortKey="Brusic, Vladimir" sort="Brusic, Vladimir" uniqKey="Brusic V" first="Vladimir" last="Brusic">Vladimir Brusic</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Department of Microbiology, Faculty of Medicine, National University of Singapore, 8 Medical Drive, 117597 Singapore</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">15215409</idno><idno type="pmc">441613</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC441613</idno><idno type="RBID">PMC:441613</idno><idno type="doi">10.1093/nar/gkh475</idno><date when="2004">2004</date><idno type="wicri:Area/Pmc/Corpus">001035</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001035</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">CysView: protein classification based on cysteine pairing patterns</title><author><name sortKey="Lenffer, Johann" sort="Lenffer, Johann" uniqKey="Lenffer J" first="Johann" last="Lenffer">Johann Lenffer</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">School of Molecular and Microbial Biosciences, Building G08, University of Sydney, NSW 2006, Australia,</nlm:aff></affiliation></author><author><name sortKey="Lai, Paulo" sort="Lai, Paulo" uniqKey="Lai P" first="Paulo" last="Lai">Paulo Lai</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">School of Molecular and Microbial Biosciences, Building G08, University of Sydney, NSW 2006, Australia,</nlm:aff></affiliation></author><author><name sortKey="El Mejaber, Wafaa" sort="El Mejaber, Wafaa" uniqKey="El Mejaber W" first="Wafaa" last="El Mejaber">Wafaa El Mejaber</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="N0x8b519a0.0x9b2ac08">IUP Génie Physiologique et Informatique, Bâtiment botanique, 40 av. Recteur Pineau-86022, Poitiers Cedex, France</nlm:aff></affiliation></author><author><name sortKey="Khan, Asif M" sort="Khan, Asif M" uniqKey="Khan A" first="Asif M." last="Khan">Asif M. Khan</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="N0x8b519a0.0x9b2ac08">Department of Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Koh, Judice L Y" sort="Koh, Judice L Y" uniqKey="Koh J" first="Judice L. Y." last="Koh">Judice L. Y. Koh</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation></author><author><name sortKey="Tan, Paul T J" sort="Tan, Paul T J" uniqKey="Tan P" first="Paul T. J." last="Tan">Paul T. J. Tan</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="N0x8b519a0.0x9b2ac08">Department of Biochemistry</nlm:aff></affiliation></author><author><name sortKey="Seah, Seng H" sort="Seah, Seng H" uniqKey="Seah S" first="Seng H." last="Seah">Seng H. Seah</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation></author><author><name sortKey="Brusic, Vladimir" sort="Brusic, Vladimir" uniqKey="Brusic V" first="Vladimir" last="Brusic">Vladimir Brusic</name><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,</nlm:aff></affiliation><affiliation><nlm:aff id="N0x8b519a0.0x9b2ac08">Department of Microbiology, Faculty of Medicine, National University of Singapore, 8 Medical Drive, 117597 Singapore</nlm:aff></affiliation></author></analytic><series><title level="j">Nucleic Acids Research</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><date when="2004">2004</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>CysView is a web-based application tool that identifies and classifies proteins according to their disulfide connectivity patterns. It accepts a dataset of annotated protein sequences in various formats and returns a graphical representation of cysteine pairing patterns. CysView displays cysteine patterns for those records in the data with disulfide annotations. It allows the viewing of records grouped by connectivity patterns. CysView's utility as an analysis tool was demonstrated by the rapid and correct classification of scorpion toxin entries from GenPept on the basis of their disulfide pairing patterns. It has proved useful for rapid detection of irrelevant and partial records, or those with incomplete annotations. CysView can be used to support distant homology between proteins. CysView is publicly available at <ext-link ext-link-type="uri" xlink:href="http://research.i2r.a-star.edu.sg/CysView/">http://research.i2r.a-star.edu.sg/CysView/</ext-link>.</p></div></front></TEI><pmc article-type="research-article"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-title>Nucleic Acids Research</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-loc>Oxford, UK</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">15215409</article-id><article-id pub-id-type="pmc">441613</article-id><article-id pub-id-type="publisher-id">gkh475</article-id><article-id pub-id-type="doi">10.1093/nar/gkh475</article-id><article-categories><subj-group subj-group-type="heading"><subject>Articles</subject></subj-group></article-categories><title-group><article-title>CysView: protein classification based on cysteine pairing patterns</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Lenffer</surname><given-names>Johann</given-names></name><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">1</xref><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">2</xref></contrib><contrib contrib-type="author"><name><surname>Lai</surname><given-names>Paulo</given-names></name><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">1</xref><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">2</xref></contrib><contrib contrib-type="author"><name><surname>El Mejaber</surname><given-names>Wafaa</given-names></name><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">1</xref><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">3</xref></contrib><contrib contrib-type="author"><name><surname>Khan</surname><given-names>Asif M.</given-names></name><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">1</xref><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">4</xref></contrib><contrib contrib-type="author"><name><surname>Koh</surname><given-names>Judice L. Y.</given-names></name><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">1</xref></contrib><contrib contrib-type="author"><name><surname>Tan</surname><given-names>Paul T. J.</given-names></name><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">1</xref><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">4</xref></contrib><contrib contrib-type="author"><name><surname>Seah</surname><given-names>Seng H.</given-names></name><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">1</xref></contrib><contrib contrib-type="author"><name><surname>Brusic</surname><given-names>Vladimir</given-names></name><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">1</xref><xref ref-type="aff" rid="N0x8b519a0.0x9b2ac08">5</xref><xref ref-type="author-notes" rid="gkh475fn1">*</xref></contrib></contrib-group><aff id="N0x8b519a0.0x9b2ac08"><label>1</label>Institute for Infocomm Research, 21 Heng Mui Keng Terrace, 119613 Singapore,<label>2</label>School of Molecular and Microbial Biosciences, Building G08, University of Sydney, NSW 2006, Australia,<label>3</label>IUP Génie Physiologique et Informatique, Bâtiment botanique, 40 av. Recteur Pineau-86022, Poitiers Cedex, France and<label>4</label>Department of Biochemistry and<label>5</label>Department of Microbiology, Faculty of Medicine, National University of Singapore, 8 Medical Drive, 117597 Singapore</aff><author-notes><fn id="gkh475fn1"><label>*</label><p>To whom correspondence should be addressed at 21 Heng Mui Keng Terrace, 119613 Singapore. Tel: +65 6874 7920; Fax: +65 6774 8056; Email: <email>vladimir@i2r.a-star.edu.sg</email></p></fn><fn id="N0x8b519a0.0x9b2ac68"><label>a</label><p>The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors</p></fn><fn id="N0x8b519a0.0x9b2ac88"><label>a</label><p>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 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.</p></fn><fn id="N0x8b519a0.0x9b2aca8"><label>a</label><p>© 2004, the authors</p></fn></author-notes><pub-date pub-type="ppub"><day>1</day><month>7</month><year>2004</year></pub-date><volume>32</volume><issue>Web Server issue</issue><fpage>W350</fpage><lpage>W355</lpage><ext-link ext-link-type="uri" xlink:href="http://www.nar.oupjournals.org/content/vol32/issueWeb Server issue//"></ext-link><history><date date-type="received"><day>15</day><month>2</month><year>2004</year></date><date date-type="rev-recd"><day>20</day><month>4</month><year>2004</year></date><date date-type="accepted"><day>3</day><month>5</month><year>2004</year></date></history><copyright-statement>Copyright © 2004 Oxford University Press</copyright-statement><copyright-year>2004</copyright-year><abstract><p>CysView is a web-based application tool that identifies and classifies proteins according to their disulfide connectivity patterns. It accepts a dataset of annotated protein sequences in various formats and returns a graphical representation of cysteine pairing patterns. CysView displays cysteine patterns for those records in the data with disulfide annotations. It allows the viewing of records grouped by connectivity patterns. CysView's utility as an analysis tool was demonstrated by the rapid and correct classification of scorpion toxin entries from GenPept on the basis of their disulfide pairing patterns. It has proved useful for rapid detection of irrelevant and partial records, or those with incomplete annotations. CysView can be used to support distant homology between proteins. CysView is publicly available at <ext-link ext-link-type="uri" xlink:href="http://research.i2r.a-star.edu.sg/CysView/">http://research.i2r.a-star.edu.sg/CysView/</ext-link>.</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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