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Biology Articles » Bioinformatics » Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource » Genome data acquisition

Genome data acquisition
- Poxvirus Bioinformatics Resource Center: a comprehensive Poxviridae informational and analytical resource

Genomic data are obtained from GenBank (13), other publiclyavailable databases and websites, as well as from ongoing sequencingprojects. The current PBRC release consists of over 35 completegenomes from the Poxviridae family of viruses. If availablefrom the GenBank record or from the sequencing laboratory, thepredicted gene set of any one genome is stored in the PBRC databaseand used as the initial starting point for annotation and curationof each genome. If a predicted gene set is not available, weperform our own gene prediction using a combination of genepredictive tools that start with open reading frames, and theninclude among others, promoter prediction, presence of functionalmotifs and assignment to orthologous protein clusters. Our experienceis that the methods used for the prediction of protein codinggenes for each poxvirus genome present in GenBank has in manycases been derived using different parameters. Therefore, weare in the process of developing a more consistent method forthe prediction of poxvirus genes and will utilize this geneprediction pipeline to reassess the gene set for each availablegenome. Each virus genome is categorized according to its genus, speciesand strain designation as determined by the International Committeefor the Taxonomy of Viruses (ICTV) (http://www.ncbi.nlm.nih.gov/ICTVdb/)(14,15). In addition to providing the nomenclature availablefrom the GenBank record for each gene in any one genome, wealso provide our own gene designation which is a combinationof the ICTV-approved species name, the strain or isolate nameand a numerical designation for each gene that starts at number1 for the left-most gene, and is incremented by one for eachsubsequent gene as determined by its genome position.

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