PlantCAZyme: a database for plant carbohydrate-active enzymes
Identifieur interne : 000E79 ( Pmc/Curation ); précédent : 000E78; suivant : 000E80PlantCAZyme: a database for plant carbohydrate-active enzymes
Auteurs : Alexander Ekstrom ; Rahil Taujale [États-Unis] ; Nathan Mcginn ; Yanbin Yin [États-Unis]Source :
- Database: The Journal of Biological Databases and Curation [ 1758-0463 ] ; 2014.
Abstract
PlantCAZyme is a database built upon dbCAN (database for automated carbohydrate active enzyme annotation), aiming to provide pre-computed sequence and annotation data of carbohydrate active enzymes (CAZymes) to plant carbohydrate and bioenergy research communities. The current version contains data of 43 790 CAZymes of 159 protein families from 35 plants (including angiosperms, gymnosperms, lycophyte and bryophyte mosses) and chlorophyte algae with fully sequenced genomes. Useful features of the database include: (i) a BLAST server and a HMMER server that allow users to search against our pre-computed sequence data for annotation purpose, (ii) a download page to allow batch downloading data of a specific CAZyme family or species and (iii) protein browse pages to provide an easy access to the most comprehensive sequence and annotation data.
Url:
DOI: 10.1093/database/bau079
PubMed: 25125445
PubMed Central: 4132414
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">PlantCAZyme: a database for plant carbohydrate-active enzymes</title><author><name sortKey="Ekstrom, Alexander" sort="Ekstrom, Alexander" uniqKey="Ekstrom A" first="Alexander" last="Ekstrom">Alexander Ekstrom</name><affiliation><nlm:aff wicri:cut=" and" id="bau079-AFF1">Department of Computer Science</nlm:aff></affiliation></author><author><name sortKey="Taujale, Rahil" sort="Taujale, Rahil" uniqKey="Taujale R" first="Rahil" last="Taujale">Rahil Taujale</name><affiliation wicri:level="1"><nlm:aff id="bau079-AFF1">Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115</wicri:regionArea></affiliation></author><author><name sortKey="Mcginn, Nathan" sort="Mcginn, Nathan" uniqKey="Mcginn N" first="Nathan" last="Mcginn">Nathan Mcginn</name><affiliation><nlm:aff wicri:cut=" and" id="bau079-AFF1">Department of Computer Science</nlm:aff></affiliation></author><author><name sortKey="Yin, Yanbin" sort="Yin, Yanbin" uniqKey="Yin Y" first="Yanbin" last="Yin">Yanbin Yin</name><affiliation wicri:level="1"><nlm:aff id="bau079-AFF1">Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">25125445</idno><idno type="pmc">4132414</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4132414</idno><idno type="RBID">PMC:4132414</idno><idno type="doi">10.1093/database/bau079</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000E80</idno><idno type="wicri:Area/Pmc/Curation">000E79</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">PlantCAZyme: a database for plant carbohydrate-active enzymes</title><author><name sortKey="Ekstrom, Alexander" sort="Ekstrom, Alexander" uniqKey="Ekstrom A" first="Alexander" last="Ekstrom">Alexander Ekstrom</name><affiliation><nlm:aff wicri:cut=" and" id="bau079-AFF1">Department of Computer Science</nlm:aff></affiliation></author><author><name sortKey="Taujale, Rahil" sort="Taujale, Rahil" uniqKey="Taujale R" first="Rahil" last="Taujale">Rahil Taujale</name><affiliation wicri:level="1"><nlm:aff id="bau079-AFF1">Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115</wicri:regionArea></affiliation></author><author><name sortKey="Mcginn, Nathan" sort="Mcginn, Nathan" uniqKey="Mcginn N" first="Nathan" last="Mcginn">Nathan Mcginn</name><affiliation><nlm:aff wicri:cut=" and" id="bau079-AFF1">Department of Computer Science</nlm:aff></affiliation></author><author><name sortKey="Yin, Yanbin" sort="Yin, Yanbin" uniqKey="Yin Y" first="Yanbin" last="Yin">Yanbin Yin</name><affiliation wicri:level="1"><nlm:aff id="bau079-AFF1">Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115</wicri:regionArea></affiliation></author></analytic><series><title level="j">Database: The Journal of Biological Databases and Curation</title><idno type="eISSN">1758-0463</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>PlantCAZyme is a database built upon dbCAN (database for automated carbohydrate active enzyme annotation), aiming to provide pre-computed sequence and annotation data of carbohydrate active enzymes (CAZymes) to plant carbohydrate and bioenergy research communities. The current version contains data of 43 790 CAZymes of 159 protein families from 35 plants (including angiosperms, gymnosperms, lycophyte and bryophyte mosses) and chlorophyte algae with fully sequenced genomes. Useful features of the database include: (i) a BLAST server and a HMMER server that allow users to search against our pre-computed sequence data for annotation purpose, (ii) a download page to allow batch downloading data of a specific CAZyme family or species and (iii) protein browse pages to provide an easy access to the most comprehensive sequence and annotation data.</p><p><bold>Database URL</bold>: <ext-link ext-link-type="uri" xlink:href="http://cys.bios.niu.edu/plantcazyme/">http://cys.bios.niu.edu/plantcazyme/</ext-link></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Rubin, E M" uniqKey="Rubin E">E.M. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Database (Oxford)</journal-id><journal-id journal-id-type="iso-abbrev">Database (Oxford)</journal-id><journal-id journal-id-type="publisher-id">database</journal-id><journal-id journal-id-type="hwp">databa</journal-id><journal-title-group><journal-title>Database: The Journal of Biological Databases and Curation</journal-title></journal-title-group><issn pub-type="epub">1758-0463</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25125445</article-id><article-id pub-id-type="pmc">4132414</article-id><article-id pub-id-type="doi">10.1093/database/bau079</article-id><article-id pub-id-type="publisher-id">bau079</article-id><article-categories><subj-group subj-group-type="heading"><subject>Database Tool</subject></subj-group></article-categories><title-group><article-title>PlantCAZyme: a database for plant carbohydrate-active enzymes</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Ekstrom</surname><given-names>Alexander</given-names></name><xref ref-type="aff" rid="bau079-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Taujale</surname><given-names>Rahil</given-names></name><xref ref-type="aff" rid="bau079-AFF1"><sup>2</sup></xref></contrib><contrib contrib-type="author"><name><surname>McGinn</surname><given-names>Nathan</given-names></name><xref ref-type="aff" rid="bau079-AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Yin</surname><given-names>Yanbin</given-names></name><xref ref-type="aff" rid="bau079-AFF1"><sup>2</sup></xref><xref ref-type="corresp" rid="bau079-COR1">*</xref></contrib><aff id="bau079-AFF1"><sup>1</sup>Department of Computer Science and<sup>2</sup>Department of Biological Sciences, Northern Illinois University, DeKalb, IL 60115, USA</aff></contrib-group><author-notes><corresp id="bau079-COR1">*Corresponding author: Tel: <phone>+1 815 753 8963</phone>; Fax: <fax>+1 815 753 7855</fax>; E-mail: <email>yyin@niu.edu</email></corresp><fn><p>Citation details: Ekstrom,A., Taujale,R., McGinn,N. <italic>et al</italic>. PlantCAZyme: a database for plant carbohydrate-active enzymes. <italic>Database</italic> (2014) Vol. 2014: article ID bau079; doi:10.1093/database/bau079</p></fn></author-notes><pub-date pub-type="collection"><year>2014</year></pub-date><pub-date pub-type="epub"><day>14</day><month>8</month><year>2014</year></pub-date><pub-date pub-type="pmc-release"><day>14</day><month>8</month><year>2014</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>2014</volume><elocation-id>bau079</elocation-id><history><date date-type="received"><day>22</day><month>2</month><year>2014</year></date><date date-type="rev-recd"><day>16</day><month>6</month><year>2014</year></date><date date-type="accepted"><day>16</day><month>6</month><year>2014</year></date></history><permissions><copyright-statement>© The Author(s) 2014. Published by Oxford University Press.</copyright-statement><copyright-year>2014</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">http://creativecommons.org/licenses/by/4.0/</ext-link>), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>PlantCAZyme is a database built upon dbCAN (database for automated carbohydrate active enzyme annotation), aiming to provide pre-computed sequence and annotation data of carbohydrate active enzymes (CAZymes) to plant carbohydrate and bioenergy research communities. The current version contains data of 43 790 CAZymes of 159 protein families from 35 plants (including angiosperms, gymnosperms, lycophyte and bryophyte mosses) and chlorophyte algae with fully sequenced genomes. Useful features of the database include: (i) a BLAST server and a HMMER server that allow users to search against our pre-computed sequence data for annotation purpose, (ii) a download page to allow batch downloading data of a specific CAZyme family or species and (iii) protein browse pages to provide an easy access to the most comprehensive sequence and annotation data.</p><p><bold>Database URL</bold>: <ext-link ext-link-type="uri" xlink:href="http://cys.bios.niu.edu/plantcazyme/">http://cys.bios.niu.edu/plantcazyme/</ext-link></p></abstract><counts><page-count count="8"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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