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

Huang Y, Lau SK, Woo PC, Yuen KY - Nucleic Acids Res. (2007)

Bottom Line: Sequences can be directly downloaded from the website in FASTA format.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Research Centre of Infection and Immunology and State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.

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.

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Related in: MedlinePlus

Screenshots of CoVDB complete genome retrieval pages. (a) Specific gene can be retrieved using the pull-down list at the left lower corner. The number in brackets indicates the number of complete genomes for that coronavirus. (b) Example of showing genomes of selected species (some group 2a coronaviruses and SARS-CoV-related coronaviruses). Default is to show the ‘Type strain’ for each species only. The columns NCBIacc and PMID link to GenBank and pubmed, respectively. (c) Example of showing S gene of selected species by choosing S in the pull-down list. For genes downstream to orf1ab, sequences upstream to the initiation codons can also be retrieved from this result page. This function is particularly useful for the detection of transcription regulatory sequences.
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Figure 2: Screenshots of CoVDB complete genome retrieval pages. (a) Specific gene can be retrieved using the pull-down list at the left lower corner. The number in brackets indicates the number of complete genomes for that coronavirus. (b) Example of showing genomes of selected species (some group 2a coronaviruses and SARS-CoV-related coronaviruses). Default is to show the ‘Type strain’ for each species only. The columns NCBIacc and PMID link to GenBank and pubmed, respectively. (c) Example of showing S gene of selected species by choosing S in the pull-down list. For genes downstream to orf1ab, sequences upstream to the initiation codons can also be retrieved from this result page. This function is particularly useful for the detection of transcription regulatory sequences.

Mentions: The main goal for setting up CoVDB is to provide a convenient and efficient platform for retrieving batches of coronavirus gene sequences. The interfaces of the database are simple and user friendly. All genes and genomes contain links to GenBank and/or pubmed. CoVDB contains two main pages for sequence retrieval. From the homepage, one can enter the first main page for retrieval of complete genomes and their genes by clicking ‘CoVDB’ (Figure 2a). From this page, users can obtain genes from specific coronavirus species by selecting the corresponding check boxes. We defined one representative genome from each species as the ‘Type strain’. Most of the time, this ‘Type strain’ is the one assigned as the reference sequence in GenBank. By choosing the ‘Type strain only’ option, users can obtain one gene sequence per species and construct phylogenetic tree or perform other comparisons. An example of retrieving complete genome or a specific gene of complete genome of selected species is shown in Figure 2b and c.Figure 2.


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

Huang Y, Lau SK, Woo PC, Yuen KY - Nucleic Acids Res. (2007)

Screenshots of CoVDB complete genome retrieval pages. (a) Specific gene can be retrieved using the pull-down list at the left lower corner. The number in brackets indicates the number of complete genomes for that coronavirus. (b) Example of showing genomes of selected species (some group 2a coronaviruses and SARS-CoV-related coronaviruses). Default is to show the ‘Type strain’ for each species only. The columns NCBIacc and PMID link to GenBank and pubmed, respectively. (c) Example of showing S gene of selected species by choosing S in the pull-down list. For genes downstream to orf1ab, sequences upstream to the initiation codons can also be retrieved from this result page. This function is particularly useful for the detection of transcription regulatory sequences.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238867&req=5

Figure 2: Screenshots of CoVDB complete genome retrieval pages. (a) Specific gene can be retrieved using the pull-down list at the left lower corner. The number in brackets indicates the number of complete genomes for that coronavirus. (b) Example of showing genomes of selected species (some group 2a coronaviruses and SARS-CoV-related coronaviruses). Default is to show the ‘Type strain’ for each species only. The columns NCBIacc and PMID link to GenBank and pubmed, respectively. (c) Example of showing S gene of selected species by choosing S in the pull-down list. For genes downstream to orf1ab, sequences upstream to the initiation codons can also be retrieved from this result page. This function is particularly useful for the detection of transcription regulatory sequences.
Mentions: The main goal for setting up CoVDB is to provide a convenient and efficient platform for retrieving batches of coronavirus gene sequences. The interfaces of the database are simple and user friendly. All genes and genomes contain links to GenBank and/or pubmed. CoVDB contains two main pages for sequence retrieval. From the homepage, one can enter the first main page for retrieval of complete genomes and their genes by clicking ‘CoVDB’ (Figure 2a). From this page, users can obtain genes from specific coronavirus species by selecting the corresponding check boxes. We defined one representative genome from each species as the ‘Type strain’. Most of the time, this ‘Type strain’ is the one assigned as the reference sequence in GenBank. By choosing the ‘Type strain only’ option, users can obtain one gene sequence per species and construct phylogenetic tree or perform other comparisons. An example of retrieving complete genome or a specific gene of complete genome of selected species is shown in Figure 2b and c.Figure 2.

Bottom Line: Sequences can be directly downloaded from the website in FASTA format.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.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, Research Centre of Infection and Immunology and State Key Laboratory of Emerging Infectious Diseases, The University of Hong Kong, Hong Kong.

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.

Show MeSH
Related in: MedlinePlus