CrusView: A Java-Based Visualization Platform for Comparative Genomics Analyses in Brassicaceae Species[OPEN]
Identifieur interne : 000340 ( Pmc/Checkpoint ); précédent : 000339; suivant : 000341CrusView: A Java-Based Visualization Platform for Comparative Genomics Analyses in Brassicaceae Species[OPEN]
Auteurs : Hao Chen ; Xiangfeng WangSource :
- Plant Physiology [ 0032-0889 ] ; 2013.
Abstract
Url:
DOI: 10.1104/pp.113.219444
PubMed: 23898041
PubMed Central: 3762655
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">CrusView: A Java-Based Visualization Platform for Comparative Genomics Analyses in Brassicaceae Species<xref ref-type="author-notes" rid="fn1"><sup>[OPEN]</sup></xref></title><author><name sortKey="Chen, Hao" sort="Chen, Hao" uniqKey="Chen H" first="Hao" last="Chen">Hao Chen</name></author><author><name sortKey="Wang, Xiangfeng" sort="Wang, Xiangfeng" uniqKey="Wang X" first="Xiangfeng" last="Wang">Xiangfeng Wang</name></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">23898041</idno><idno type="pmc">3762655</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762655</idno><idno type="RBID">PMC:3762655</idno><idno type="doi">10.1104/pp.113.219444</idno><date when="2013">2013</date><idno type="wicri:Area/Pmc/Corpus">000382</idno><idno type="wicri:Area/Pmc/Curation">000382</idno><idno type="wicri:Area/Pmc/Checkpoint">000340</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">CrusView: A Java-Based Visualization Platform for Comparative Genomics Analyses in Brassicaceae Species<xref ref-type="author-notes" rid="fn1"><sup>[OPEN]</sup></xref></title><author><name sortKey="Chen, Hao" sort="Chen, Hao" uniqKey="Chen H" first="Hao" last="Chen">Hao Chen</name></author><author><name sortKey="Wang, Xiangfeng" sort="Wang, Xiangfeng" uniqKey="Wang X" first="Xiangfeng" last="Wang">Xiangfeng Wang</name></author></analytic><series><title level="j">Plant Physiology</title><idno type="ISSN">0032-0889</idno><idno type="eISSN">1532-2548</idno><imprint><date when="2013">2013</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><italic>CrusView integrates karyotype information when comparing two genomes, which allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of Brassicaceae genomes</italic>.</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">Plant Physiol</journal-id><journal-id journal-id-type="iso-abbrev">Plant Physiol</journal-id><journal-id journal-id-type="hwp">plantphysiol</journal-id><journal-id journal-id-type="publisher-id">aspb</journal-id><journal-title-group><journal-title>Plant Physiology</journal-title></journal-title-group><issn pub-type="ppub">0032-0889</issn><issn pub-type="epub">1532-2548</issn><publisher><publisher-name>American Society of Plant Biologists</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">23898041</article-id><article-id pub-id-type="pmc">3762655</article-id><article-id pub-id-type="publisher-id">219444</article-id><article-id pub-id-type="doi">10.1104/pp.113.219444</article-id><article-categories><subj-group subj-group-type="heading"><subject>Systems and Synthetic Biology</subject></subj-group></article-categories><title-group><article-title>CrusView: A Java-Based Visualization Platform for Comparative Genomics Analyses in Brassicaceae Species<xref ref-type="author-notes" rid="fn1"><sup>[OPEN]</sup></xref></article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Chen</surname><given-names>Hao</given-names></name><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0003-1224-0688</contrib-id></contrib><contrib contrib-type="author"><name><surname>Wang</surname><given-names>Xiangfeng</given-names></name><xref ref-type="corresp" rid="cor1">*</xref><contrib-id contrib-id-type="orcid">http://orcid.org/0000-0002-6406-5597</contrib-id></contrib><aff id="aff1">School of Plant Sciences, University of Arizona, Tucson, Arizona, 85721</aff></contrib-group><author-notes><corresp id="cor1"><label>*</label>Address correspondence to <email>xwang1@cals.arizona.edu</email>.</corresp><fn id="afn1"><p>The author responsible for distribution of materials integral to the findings presented in this article in accordance with the policy described in the Instructions for Authors (<ext-link ext-link-type="uri" xlink:href="http://www.plantphysiol.org">www.plantphysiol.org</ext-link>) is: Xiangfeng Wang (<email>xwang1@cals.arizona.edu</email>).</p></fn><fn id="fn1"><label>[OPEN]</label><p>Articles can be viewed online without a subscription.</p></fn><fn><p><ext-link ext-link-type="uri" xlink:href="http://www.plantphysiol.org/cgi/doi/10.1104/pp.113.219444">www.plantphysiol.org/cgi/doi/10.1104/pp.113.219444</ext-link></p></fn></author-notes><pmc-comment>Fake ppub date generated by PMC from publisher
pub-date/@pub-type='epub-ppub' </pmc-comment>
<pub-date pub-type="ppub"><month>9</month><year>2013</year></pub-date><pub-date pub-type="epub"><day>29</day><month>7</month><year>2013</year></pub-date><pub-date pub-type="pmc-release"><day>29</day><month>7</month><year>2013</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>163</volume><issue>1</issue><fpage>354</fpage><lpage>362</lpage><history><date date-type="received"><day>10</day><month>4</month><year>2013</year></date><date date-type="accepted"><day>20</day><month>7</month><year>2013</year></date></history><permissions><copyright-statement>© 2013 American Society of Plant Biologists. All Rights Reserved.</copyright-statement><copyright-year>2013</copyright-year></permissions><self-uri xlink:role="icon" xlink:type="simple" xlink:href="PP_219444_ic1.gif"></self-uri><abstract abstract-type="precis"><p><italic>CrusView integrates karyotype information when comparing two genomes, which allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of Brassicaceae genomes</italic>.</p></abstract><abstract><p>In plants and animals, chromosomal breakage and fusion events based on conserved syntenic genomic blocks lead to conserved patterns of karyotype evolution among species of the same family. However, karyotype information has not been well utilized in genomic comparison studies. We present CrusView, a Java-based bioinformatic application utilizing Standard Widget Toolkit/Swing graphics libraries and a SQLite database for performing visualized analyses of comparative genomics data in Brassicaceae (crucifer) plants. Compared with similar software and databases, one of the unique features of CrusView is its integration of karyotype information when comparing two genomes. This feature allows users to perform karyotype-based genome assembly and karyotype-assisted genome synteny analyses with preset karyotype patterns of the Brassicaceae genomes. Additionally, CrusView is a local program, which gives its users high flexibility when analyzing unpublished genomes and allows users to upload self-defined genomic information so that they can visually study the associations between genome structural variations and genetic elements, including chromosomal rearrangements, genomic macrosynteny, gene families, high-frequency recombination sites, and tandem and segmental duplications between related species. This tool will greatly facilitate karyotype, chromosome, and genome evolution studies using visualized comparative genomics approaches in Brassicaceae species. CrusView is freely available at <ext-link ext-link-type="uri" xlink:href="http://www.cmbb.arizona.edu/CrusView/">http://www.cmbb.arizona.edu/CrusView/</ext-link>.</p></abstract><counts><page-count count="9"></page-count></counts></article-meta><notes><glossary><title>Glossary</title><def-list><def-item><term id="term1">CCP</term><def id="def1"><p>comparative chromosomal painting</p></def></def-item><def-item><term id="term2">GUI</term><def id="def2"><p>graphical user interface</p></def></def-item><def-item><term id="term3">ID</term><def id="def3"><p>gene identifier</p></def></def-item><def-item><term id="term4">CentO</term><def id="def4"><p>centromere-specific</p></def></def-item></def-list></glossary></notes></front></pmc><affiliations><list></list><tree><noCountry><name sortKey="Chen, Hao" sort="Chen, Hao" uniqKey="Chen H" first="Hao" last="Chen">Hao Chen</name><name sortKey="Wang, Xiangfeng" sort="Wang, Xiangfeng" uniqKey="Wang X" first="Xiangfeng" last="Wang">Xiangfeng Wang</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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