PLAZA 3.0: an access point for plant comparative genomics
Identifieur interne : 000981 ( Main/Exploration ); précédent : 000980; suivant : 000982PLAZA 3.0: an access point for plant comparative genomics
Auteurs : Sebastian Proost [Allemagne] ; Michiel Van Bel [Belgique] ; Dries Vaneechoutte [Belgique] ; Yves Van De Peer [Belgique, Afrique du Sud] ; Dirk Inzé [Belgique] ; Bernd Mueller-Roeber [Allemagne] ; Klaas Vandepoele [Belgique]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2014.
Abstract
Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (
Url:
DOI: 10.1093/nar/gku986
PubMed: 25324309
PubMed Central: 4384038
Affiliations:
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xml:lang="fr">Belgique</country><wicri:regionArea>VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF4">Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Vaneechoutte, Dries" sort="Vaneechoutte, Dries" uniqKey="Vaneechoutte D" first="Dries" last="Vaneechoutte">Dries Vaneechoutte</name><affiliation wicri:level="1"><nlm:aff id="AFF3">VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>VIB, Department of Plant Systems Biology, Technologiepark 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id="AFF4">Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF5">Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028, South Africa</nlm:aff><country xml:lang="fr">Afrique du Sud</country><wicri:regionArea>Genomics Research Institute (GRI), University of Pretoria, Private bag X20, Pretoria, 0028</wicri:regionArea><wicri:noRegion>0028</wicri:noRegion></affiliation></author><author><name sortKey="Inze, Dirk" sort="Inze, Dirk" uniqKey="Inze D" first="Dirk" last="Inzé">Dirk Inzé</name><affiliation wicri:level="1"><nlm:aff id="AFF3">VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF4">Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation></author><author><name sortKey="Mueller Roeber, Bernd" sort="Mueller Roeber, Bernd" uniqKey="Mueller Roeber B" first="Bernd" last="Mueller-Roeber">Bernd Mueller-Roeber</name><affiliation wicri:level="1"><nlm:aff id="AFF1">University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße 24-25, Haus 20, 14476 Potsdam-Golm</wicri:regionArea><wicri:noRegion>14476 Potsdam-Golm</wicri:noRegion><wicri:noRegion>14476 Potsdam-Golm</wicri:noRegion><wicri:noRegion>14476 Potsdam-Golm</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF2">Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany</nlm:aff><country xml:lang="fr">Allemagne</country><wicri:regionArea>Max-Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm</wicri:regionArea><wicri:noRegion>14476 Potsdam-Golm</wicri:noRegion><wicri:noRegion>14476 Potsdam-Golm</wicri:noRegion><wicri:noRegion>14476 Potsdam-Golm</wicri:noRegion></affiliation></author><author><name sortKey="Vandepoele, Klaas" sort="Vandepoele, Klaas" uniqKey="Vandepoele K" first="Klaas" last="Vandepoele">Klaas Vandepoele</name><affiliation wicri:level="1"><nlm:aff id="AFF3">VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>VIB, Department of Plant Systems Biology, Technologiepark 927, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF4">Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent, Belgium</nlm:aff><country xml:lang="fr">Belgique</country><wicri:regionArea>Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, Ghent</wicri:regionArea><wicri:noRegion>Ghent</wicri:noRegion></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="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (<ext-link ext-link-type="uri" xlink:href="http://bioinformatics.psb.ugent.be/plaza/">http://bioinformatics.psb.ugent.be/plaza/</ext-link>) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Van De Peer, Y" uniqKey="Van De Peer Y">Y. Van de Peer</name></author><author><name sortKey="Pires, J C" uniqKey="Pires J">J.C. Pires</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Leeggangers, H A" uniqKey="Leeggangers H">H.A. Leeggangers</name></author><author><name sortKey="Moreno Pachon, N" uniqKey="Moreno Pachon N">N. Moreno-Pachon</name></author><author><name sortKey="Gude, H" uniqKey="Gude H">H. Gude</name></author><author><name sortKey="Immink, R G" uniqKey="Immink R">R.G. 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Gascuel</name></author></analytic></biblStruct></listBibl></div1></back></TEI><affiliations><list><country><li>Afrique du Sud</li><li>Allemagne</li><li>Belgique</li></country></list><tree><country name="Allemagne"><noRegion><name sortKey="Proost, Sebastian" sort="Proost, Sebastian" uniqKey="Proost S" first="Sebastian" last="Proost">Sebastian Proost</name></noRegion><name sortKey="Mueller Roeber, Bernd" sort="Mueller Roeber, Bernd" uniqKey="Mueller Roeber B" first="Bernd" last="Mueller-Roeber">Bernd Mueller-Roeber</name><name sortKey="Mueller Roeber, Bernd" sort="Mueller Roeber, Bernd" uniqKey="Mueller Roeber B" first="Bernd" last="Mueller-Roeber">Bernd Mueller-Roeber</name><name sortKey="Proost, Sebastian" sort="Proost, Sebastian" uniqKey="Proost S" first="Sebastian" last="Proost">Sebastian Proost</name></country><country name="Belgique"><noRegion><name sortKey="Van Bel, Michiel" sort="Van Bel, Michiel" uniqKey="Van Bel M" first="Michiel" last="Van Bel">Michiel Van Bel</name></noRegion><name sortKey="Inze, Dirk" sort="Inze, Dirk" uniqKey="Inze D" first="Dirk" last="Inzé">Dirk Inzé</name><name sortKey="Inze, Dirk" sort="Inze, Dirk" uniqKey="Inze D" first="Dirk" last="Inzé">Dirk Inzé</name><name sortKey="Van Bel, Michiel" sort="Van Bel, Michiel" uniqKey="Van Bel M" first="Michiel" last="Van Bel">Michiel Van Bel</name><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name><name sortKey="Vandepoele, Klaas" sort="Vandepoele, Klaas" uniqKey="Vandepoele K" first="Klaas" last="Vandepoele">Klaas Vandepoele</name><name sortKey="Vandepoele, Klaas" sort="Vandepoele, Klaas" uniqKey="Vandepoele K" first="Klaas" last="Vandepoele">Klaas Vandepoele</name><name sortKey="Vaneechoutte, Dries" sort="Vaneechoutte, Dries" uniqKey="Vaneechoutte D" first="Dries" last="Vaneechoutte">Dries Vaneechoutte</name><name sortKey="Vaneechoutte, Dries" sort="Vaneechoutte, Dries" uniqKey="Vaneechoutte D" first="Dries" last="Vaneechoutte">Dries Vaneechoutte</name></country><country name="Afrique du Sud"><noRegion><name sortKey="Van De Peer, Yves" sort="Van De Peer, Yves" uniqKey="Van De Peer Y" first="Yves" last="Van De Peer">Yves Van De Peer</name></noRegion></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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