CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes
Identifieur interne : 000F86 ( Pmc/Checkpoint ); précédent : 000F85; suivant : 000F87CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes
Auteurs : Yi Huang ; Susanna K. P. Lau [Hong Kong] ; Patrick C. Y. Woo [Hong Kong] ; Kwok-Yung Yuen [Hong Kong]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2007.
Abstract
The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (
Url:
DOI: 10.1093/nar/gkm754
PubMed: 17913743
PubMed Central: 2238867
Affiliations:
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Lau</name><affiliation><nlm:aff id="AFF1">Department of Microbiology,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="AFF1">Research Centre of Infection and Immunology</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF1">State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</wicri:regionArea><wicri:noRegion>The University of Hong Kong</wicri:noRegion></affiliation></author><author><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. Y." last="Woo">Patrick C. Y. Woo</name><affiliation><nlm:aff id="AFF1">Department of Microbiology,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="AFF1">Research Centre of Infection and Immunology</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF1">State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</wicri:regionArea><wicri:noRegion>The University of Hong Kong</wicri:noRegion></affiliation></author><author><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><affiliation><nlm:aff id="AFF1">Department of Microbiology,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="AFF1">Research Centre of Infection and Immunology</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF1">State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</wicri:regionArea><wicri:noRegion>The University of Hong Kong</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">17913743</idno><idno type="pmc">2238867</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238867</idno><idno type="RBID">PMC:2238867</idno><idno type="doi">10.1093/nar/gkm754</idno><date when="2007">2007</date><idno type="wicri:Area/Pmc/Corpus">001307</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">001307</idno><idno type="wicri:Area/Pmc/Curation">001307</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">001307</idno><idno type="wicri:Area/Pmc/Checkpoint">000F86</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">000F86</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes</title><author><name sortKey="Huang, Yi" sort="Huang, Yi" uniqKey="Huang Y" first="Yi" last="Huang">Yi Huang</name><affiliation><nlm:aff id="AFF1">Department of Microbiology,</nlm:aff></affiliation></author><author><name sortKey="Lau, Susanna K P" sort="Lau, Susanna K P" uniqKey="Lau S" first="Susanna K. P." last="Lau">Susanna K. P. Lau</name><affiliation><nlm:aff id="AFF1">Department of Microbiology,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="AFF1">Research Centre of Infection and Immunology</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF1">State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</wicri:regionArea><wicri:noRegion>The University of Hong Kong</wicri:noRegion></affiliation></author><author><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. Y." last="Woo">Patrick C. Y. Woo</name><affiliation><nlm:aff id="AFF1">Department of Microbiology,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="AFF1">Research Centre of Infection and Immunology</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF1">State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</wicri:regionArea><wicri:noRegion>The University of Hong Kong</wicri:noRegion></affiliation></author><author><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name><affiliation><nlm:aff id="AFF1">Department of Microbiology,</nlm:aff></affiliation><affiliation><nlm:aff wicri:cut=" and" id="AFF1">Research Centre of Infection and Immunology</nlm:aff></affiliation><affiliation wicri:level="1"><nlm:aff id="AFF1">State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</nlm:aff><country xml:lang="fr">Hong Kong</country><wicri:regionArea>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</wicri:regionArea><wicri:noRegion>The University of Hong Kong</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="2007">2007</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (<ext-link ext-link-type="uri" xlink:href="http://covdb.microbiology.hku.hk">http://covdb.microbiology.hku.hk</ext-link>), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. Sequences can be directly downloaded from the website in FASTA format. CoVDB also provides detailed annotation of all coronavirus sequences using a standardized nomenclature system, and overcomes the problems of duplicated and identical sequences in other databases. For complete genomes, a single representative sequence for each species is available for comparative analysis such as phylogenetic studies. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Nucleic Acids Res</journal-id><journal-id journal-id-type="iso-abbrev">Nucleic Acids Res</journal-id><journal-id journal-id-type="publisher-id">nar</journal-id><journal-id journal-id-type="hwp">nar</journal-id><journal-title-group><journal-title>Nucleic Acids Research</journal-title></journal-title-group><issn pub-type="ppub">0305-1048</issn><issn pub-type="epub">1362-4962</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">17913743</article-id><article-id pub-id-type="pmc">2238867</article-id><article-id pub-id-type="doi">10.1093/nar/gkm754</article-id><article-categories><subj-group subj-group-type="heading"><subject>Articles</subject></subj-group></article-categories><title-group><article-title>CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Huang</surname><given-names>Yi</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref></contrib><contrib contrib-type="author"><name><surname>Lau</surname><given-names>Susanna K. P.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref><xref ref-type="aff" rid="AFF1"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Woo</surname><given-names>Patrick C. Y.</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref><xref ref-type="aff" rid="AFF1"><sup>3</sup></xref><xref ref-type="corresp" rid="COR1">*</xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Yuen</surname><given-names>Kwok-yung</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref><xref ref-type="aff" rid="AFF1"><sup>3</sup></xref></contrib></contrib-group><aff id="AFF1"><sup>1</sup>Department of Microbiology,<sup>2</sup>Research Centre of Infection and Immunology and<sup>3</sup>State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong</aff><author-notes><corresp id="COR1">*To whom correspondence should be addressed.<phone>852 2855 4892</phone><fax>852 2855 1241</fax><email>pcywoo@hkucc.hku.hk</email> Correspondence may also be addressed to Kwok-yung Yuen.<phone>852 2855 4892</phone><fax>852 2855 1241</fax><email>hkumicro@hkucc.hku.hk</email></corresp></author-notes><pub-date pub-type="ppub"><month>1</month><year>2008</year></pub-date><pub-date pub-type="epub"><day>2</day><month>10</month><year>2007</year></pub-date><pub-date pub-type="pmc-release"><day>2</day><month>10</month><year>2007</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>36</volume><issue>Database issue</issue><issue-title>Database issue</issue-title><fpage>D504</fpage><lpage>D511</lpage><history><date date-type="received"><day>27</day><month>6</month><year>2007</year></date><date date-type="rev-recd"><day>24</day><month>8</month><year>2007</year></date><date date-type="accepted"><day>11</day><month>9</month><year>2007</year></date></history><permissions><copyright-statement>© 2007 The Author(s)</copyright-statement><copyright-year>2007</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/2.0/uk/">http://creativecommons.org/licenses/by-nc/2.0/uk/</ext-link>) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p>The recent SARS epidemic has boosted interest in the discovery of novel human and animal coronaviruses. By July 2007, more than 3000 coronavirus sequence records, including 264 complete genomes, are available in GenBank. The number of coronavirus species with complete genomes available has increased from 9 in 2003 to 25 in 2007, of which six, including coronavirus HKU1, bat SARS coronavirus, group 1 bat coronavirus HKU2, groups 2c and 2d coronaviruses, were sequenced by our laboratory. To overcome the problems we encountered in the existing databases during comparative sequence analysis, we built a comprehensive database, CoVDB (<ext-link ext-link-type="uri" xlink:href="http://covdb.microbiology.hku.hk">http://covdb.microbiology.hku.hk</ext-link>), of annotated coronavirus genes and genomes. CoVDB provides a convenient platform for rapid and accurate batch sequence retrieval, the cornerstone and bottleneck for comparative gene or genome analysis. Sequences can be directly downloaded from the website in FASTA format. CoVDB also provides detailed annotation of all coronavirus sequences using a standardized nomenclature system, and overcomes the problems of duplicated and identical sequences in other databases. For complete genomes, a single representative sequence for each species is available for comparative analysis such as phylogenetic studies. With the annotated sequences in CoVDB, more specific blast search results can be generated for efficient downstream analysis.</p></abstract></article-meta></front></pmc><affiliations><list><country><li>Hong Kong</li></country></list><tree><noCountry><name sortKey="Huang, Yi" sort="Huang, Yi" uniqKey="Huang Y" first="Yi" last="Huang">Yi Huang</name></noCountry><country name="Hong Kong"><noRegion><name sortKey="Lau, Susanna K P" sort="Lau, Susanna K P" uniqKey="Lau S" first="Susanna K. P." last="Lau">Susanna K. P. Lau</name></noRegion><name sortKey="Woo, Patrick C Y" sort="Woo, Patrick C Y" uniqKey="Woo P" first="Patrick C. Y." last="Woo">Patrick C. Y. Woo</name><name sortKey="Yuen, Kwok Yung" sort="Yuen, Kwok Yung" uniqKey="Yuen K" first="Kwok-Yung" last="Yuen">Kwok-Yung Yuen</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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