CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes
Identifieur interne : 003836 ( Main/Exploration ); précédent : 003835; suivant : 003837CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes
Auteurs : Yi Huang [Hong Kong] ; Susanna K. P. Lau [Hong Kong] ; Patrick C. Y. Woo [Hong Kong] ; Kwok-Yung Yuen [Hong Kong]Source :
- Nucleic Acids Research [ 0305-1048 ] ; 2008.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- chemical , chemistry : Viral Proteins.
- genetics : Coronavirus, Viral Proteins.
- Computational Biology, Databases, Genetic, Genes, Viral, Genome, Viral, Genomics, Internet.
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 (http://covdb.microbiology.hku.hk), 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.
Url:
- https://api.istex.fr/ark:/67375/HXZ-Z08HWLP4-C/fulltext.pdf
- http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238867
DOI: 10.1093/nar/gkm754
Affiliations:
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Le document en format XML
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Woo</name><affiliation wicri:level="1"><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Department of Microbiology, Research Centre of Infection and Immunology and State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</wicri:regionArea><wicri:noRegion>The University of Hong Kong</wicri:noRegion></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Hong Kong</country></affiliation><affiliation></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 wicri:level="1"><country xml:lang="fr">Hong Kong</country><wicri:regionArea>Department of Microbiology, Research Centre of Infection and Immunology and State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong</wicri:regionArea><wicri:noRegion>The University of Hong Kong</wicri:noRegion></affiliation><affiliation wicri:level="1"><country wicri:rule="url">Hong Kong</country></affiliation></author></analytic><monogr></monogr><series><title level="j" type="main">Nucleic Acids Research</title><title level="j" type="issue">Database issue</title><idno type="ISSN">0305-1048</idno><idno type="eISSN">1362-4962</idno><imprint><publisher>Oxford University Press</publisher><date type="published">2008</date><date type="e-published">2007</date><biblScope unit="vol">36</biblScope><biblScope unit="issue">suppl_1</biblScope><biblScope unit="page" from="D504">D504</biblScope><biblScope unit="page" to="D511">D511</biblScope></imprint><idno type="ISSN">0305-1048</idno></series></biblStruct></sourceDesc><seriesStmt><idno type="ISSN">0305-1048</idno></seriesStmt></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Computational Biology</term><term>Coronavirus (genetics)</term><term>Databases, Genetic</term><term>Genes, Viral</term><term>Genome, Viral</term><term>Genomics</term><term>Internet</term><term>Viral Proteins (chemistry)</term><term>Viral Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Bases de données génétiques</term><term>Biologie informatique</term><term>Coronavirus (génétique)</term><term>Gènes viraux</term><term>Génome viral</term><term>Génomique</term><term>Internet</term><term>Protéines virales ()</term><term>Protéines virales (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="chemistry" xml:lang="en"><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Coronavirus</term><term>Viral Proteins</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus</term><term>Protéines virales</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Computational Biology</term><term>Databases, Genetic</term><term>Genes, Viral</term><term>Genome, Viral</term><term>Genomics</term><term>Internet</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Bases de données génétiques</term><term>Biologie informatique</term><term>Gènes viraux</term><term>Génome viral</term><term>Génomique</term><term>Internet</term><term>Protéines virales</term></keywords></textClass></profileDesc></teiHeader><front><div type="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 (http://covdb.microbiology.hku.hk), 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.</div></front></TEI><affiliations><list><country><li>Hong Kong</li></country></list><tree><country name="Hong Kong"><noRegion><name sortKey="Huang, Yi" sort="Huang, Yi" uniqKey="Huang Y" first="Yi" last="Huang">Yi Huang</name></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><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="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><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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