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Article: CoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes

TitleCoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomes
Authors
Issue Date2008
PublisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/
Citation
Nucleic Acids Research, 2008, v. 36 suppl. 1, p. D504-D511 How to Cite?
AbstractThe 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. © 2007 The Author(s).
Persistent Identifierhttp://hdl.handle.net/10722/157503
ISSN
2015 Impact Factor: 9.202
2015 SCImago Journal Rankings: 7.458
PubMed Central ID
ISI Accession Number ID
References

 

DC FieldValueLanguage
dc.contributor.authorHuang, Yen_US
dc.contributor.authorLau, SKPen_US
dc.contributor.authorWoo, PCYen_US
dc.contributor.authorYuen, KYen_US
dc.date.accessioned2012-08-08T08:50:38Z-
dc.date.available2012-08-08T08:50:38Z-
dc.date.issued2008en_US
dc.identifier.citationNucleic Acids Research, 2008, v. 36 suppl. 1, p. D504-D511en_US
dc.identifier.issn0305-1048en_US
dc.identifier.urihttp://hdl.handle.net/10722/157503-
dc.description.abstractThe 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. © 2007 The Author(s).en_US
dc.languageengen_US
dc.publisherOxford University Press. The Journal's web site is located at http://nar.oxfordjournals.org/en_US
dc.relation.ispartofNucleic Acids Researchen_US
dc.rightsNucleic Acids Research. Copyright © Oxford University Press.-
dc.subject.meshComputational Biologyen_US
dc.subject.meshCoronavirus - Geneticsen_US
dc.subject.meshDatabases, Geneticen_US
dc.subject.meshGenes, Viralen_US
dc.subject.meshGenome, Viralen_US
dc.subject.meshGenomicsen_US
dc.subject.meshInterneten_US
dc.subject.meshViral Proteins - Chemistry - Geneticsen_US
dc.titleCoVDB: a comprehensive database for comparative analysis of coronavirus genes and genomesen_US
dc.typeArticleen_US
dc.identifier.emailHuang, Y: huangyi@hkucc.hku.hken_US
dc.identifier.emailLau, SKP: skplau@hkucc.hku.hken_US
dc.identifier.emailWoo, PCY: pcywoo@hkucc.hku.hken_US
dc.identifier.emailYuen, KY: kyyuen@hkucc.hku.hk-
dc.identifier.authorityLau, SKP=rp00486en_US
dc.identifier.authorityWoo, PCY=rp00430en_US
dc.identifier.authorityYuen, KY=rp00366en_US
dc.description.naturelink_to_OA_fulltexten_US
dc.identifier.doi10.1093/nar/gkm754en_US
dc.identifier.pmid17913743-
dc.identifier.pmcidPMC2238867-
dc.identifier.scopuseid_2-s2.0-38549130737en_US
dc.identifier.hkuros149571-
dc.relation.referenceshttp://www.scopus.com/mlt/select.url?eid=2-s2.0-38549130737&selection=ref&src=s&origin=recordpageen_US
dc.identifier.volume36en_US
dc.identifier.issuesuppl. 1en_US
dc.identifier.spageD504en_US
dc.identifier.epageD511en_US
dc.identifier.isiWOS:000252545400090-
dc.publisher.placeUnited Kingdomen_US
dc.identifier.scopusauthoridHuang, Y=35597414700en_US
dc.identifier.scopusauthoridLau, SKP=7401596211en_US
dc.identifier.scopusauthoridWoo, PCY=7201801340en_US
dc.identifier.scopusauthoridYuen, KY=36078079100en_US
dc.customcontrol.immutablesml 130529-

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