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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Using the Generic Synteny Browser (GBrowse_syn)</title><author><name sortKey="Mckay, Sheldon J" sort="Mckay, Sheldon J" uniqKey="Mckay S" first="Sheldon J." last="Mckay">Sheldon J. Mckay</name><affiliation><nlm:aff id="A1"> Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA</nlm:aff></affiliation></author><author><name sortKey="Vergara, Ismael A" sort="Vergara, Ismael A" uniqKey="Vergara I" first="Ismael A." last="Vergara">Ismael A. Vergara</name><affiliation><nlm:aff id="A2"> Simon Fraser University, Burnaby, BC, Canada</nlm:aff></affiliation></author><author><name sortKey="Stajich, Jason E" sort="Stajich, Jason E" uniqKey="Stajich J" first="Jason E." last="Stajich">Jason E. Stajich</name><affiliation><nlm:aff id="A3"> University of California Riverside, CA, USA</nlm:aff></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">20836076</idno><idno type="pmc">3162311</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3162311</idno><idno type="RBID">PMC:3162311</idno><idno type="doi">10.1002/0471250953.bi0912s31</idno><date when="2010">2010</date><idno type="wicri:Area/Pmc/Corpus">000318</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Using the Generic Synteny Browser (GBrowse_syn)</title><author><name sortKey="Mckay, Sheldon J" sort="Mckay, Sheldon J" uniqKey="Mckay S" first="Sheldon J." last="Mckay">Sheldon J. Mckay</name><affiliation><nlm:aff id="A1"> Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA</nlm:aff></affiliation></author><author><name sortKey="Vergara, Ismael A" sort="Vergara, Ismael A" uniqKey="Vergara I" first="Ismael A." last="Vergara">Ismael A. Vergara</name><affiliation><nlm:aff id="A2"> Simon Fraser University, Burnaby, BC, Canada</nlm:aff></affiliation></author><author><name sortKey="Stajich, Jason E" sort="Stajich, Jason E" uniqKey="Stajich J" first="Jason E." last="Stajich">Jason E. Stajich</name><affiliation><nlm:aff id="A3"> University of California Riverside, CA, USA</nlm:aff></affiliation></author></analytic><series><title level="j">Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]</title><idno type="ISSN">1934-3396</idno><idno type="eISSN">1934-340X</idno><imprint><date when="2010">2010</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p id="P1">Genome Browsers are software that allow the user to view genome annotations in the context of a reference sequence, such as a chromosome, contig, scaffold, etc. The Generic Genome Browser (GBrowse) is an open source genome browser package developed as part of the Generic Model Database Project (see Unit 9.9; <xref ref-type="bibr" rid="R7">Stein et at., 2002</xref>). The increasing number of sequenced genomes has to a corresponding growth in the field of comparative genomics, which requires methods to view and compare multiple genomes. Using the same software framework as GBrowse, the Generic Synteny Browser (GBrowse_syn) allows the comparison of co-linear regions of multiple genomes using the familiar GBrowse-style web page. Like GBrowse, GBrowse_syn can be configured to display any organism and is currently the synteny browser used for model organisms such as <italic>C. elegans</italic> (WormBase; <ext-link ext-link-type="uri" xlink:href="http://www.wormbase.org">www.wormbase.org</ext-link>; see Unit 1.8) and <italic>Arabidopsis</italic> (TAIR; <ext-link ext-link-type="uri" xlink:href="http://www.arabidopsis.org">www.arabidopsis.org</ext-link>; see Unit 1.11). GBrowse_syn is part of the GBrowse software package and can be downloaded from the web and run on any unix-like operating system, such as Linux, Solaris, Mac OS X etc. GBrowse_syn is still under active development. This unit will cover installation and configuration as part of the current stable version of GBrowse (v1.71).</p></div></front></TEI><pmc article-type="research-article" xml:lang="en"><pmc-comment>The publisher of this article does not allow downloading of the full text in XML form.</pmc-comment>
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<front><journal-meta><journal-id journal-id-type="nlm-journal-id">101157830</journal-id><journal-id journal-id-type="pubmed-jr-id">34237</journal-id><journal-id journal-id-type="nlm-ta">Curr Protoc Bioinformatics</journal-id><journal-title-group><journal-title>Current protocols in bioinformatics / editoral board, Andreas D. Baxevanis ... [et al.]</journal-title></journal-title-group><issn pub-type="ppub">1934-3396</issn><issn pub-type="epub">1934-340X</issn></journal-meta><article-meta><article-id pub-id-type="pmid">20836076</article-id><article-id pub-id-type="pmc">3162311</article-id><article-id pub-id-type="doi">10.1002/0471250953.bi0912s31</article-id><article-id pub-id-type="manuscript">NIHMS234286</article-id><article-categories><subj-group subj-group-type="heading"><subject>Article</subject></subj-group></article-categories><title-group><article-title>Using the Generic Synteny Browser (GBrowse_syn)</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>McKay</surname><given-names>Sheldon J.</given-names></name><xref rid="A1" ref-type="aff">1</xref><xref rid="FN1" ref-type="author-notes">2</xref></contrib><contrib contrib-type="author"><name><surname>Vergara</surname><given-names>Ismael A.</given-names></name><xref rid="A2" ref-type="aff">3</xref></contrib><contrib contrib-type="author"><name><surname>Stajich</surname><given-names>Jason E.</given-names></name><xref rid="A3" ref-type="aff">4</xref></contrib></contrib-group><aff id="A1"><label>1</label> Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA</aff><aff id="A2"><label>3</label> Simon Fraser University, Burnaby, BC, Canada</aff><aff id="A3"><label>4</label> University of California Riverside, CA, USA</aff><author-notes><fn id="FN1" fn-type="present-address"><label>2</label><p>Current Address: University of Arizona, Tucson, AZ, USA</p></fn></author-notes><pub-date pub-type="nihms-submitted"><day>28</day><month>3</month><year>2011</year></pub-date><pub-date pub-type="ppub"><month>9</month><year>2010</year></pub-date><pub-date pub-type="pmc-release"><day>26</day><month>8</month><year>2011</year></pub-date><volume>CHAPTER</volume><fpage>Unit</fpage><lpage>9.12</lpage><abstract><p id="P1">Genome Browsers are software that allow the user to view genome annotations in the context of a reference sequence, such as a chromosome, contig, scaffold, etc. The Generic Genome Browser (GBrowse) is an open source genome browser package developed as part of the Generic Model Database Project (see Unit 9.9; <xref ref-type="bibr" rid="R7">Stein et at., 2002</xref>). The increasing number of sequenced genomes has to a corresponding growth in the field of comparative genomics, which requires methods to view and compare multiple genomes. Using the same software framework as GBrowse, the Generic Synteny Browser (GBrowse_syn) allows the comparison of co-linear regions of multiple genomes using the familiar GBrowse-style web page. Like GBrowse, GBrowse_syn can be configured to display any organism and is currently the synteny browser used for model organisms such as <italic>C. elegans</italic> (WormBase; <ext-link ext-link-type="uri" xlink:href="http://www.wormbase.org">www.wormbase.org</ext-link>; see Unit 1.8) and <italic>Arabidopsis</italic> (TAIR; <ext-link ext-link-type="uri" xlink:href="http://www.arabidopsis.org">www.arabidopsis.org</ext-link>; see Unit 1.11). GBrowse_syn is part of the GBrowse software package and can be downloaded from the web and run on any unix-like operating system, such as Linux, Solaris, Mac OS X etc. GBrowse_syn is still under active development. This unit will cover installation and configuration as part of the current stable version of GBrowse (v1.71).</p></abstract></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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