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

Huang, Yi; Lau, Susanna K. P.; Woo, Patrick C. Y.; Yuen, Kwok-yung

By July 2007, more than 3000 coronavirus sequence records, including a total of 264 complete genomes, are available in GenBank (24) . Among the 25 coronavirus species with complete genome sequence available, six were sequenced by our group, including CoV-HKU1 and bat SARS-CoV (13, 16, 18, 19) . Furthermore, we defined two novel subgroups of group 2 coronavirus (18) . During the process of batch sequence retrieval for comparative genome analysis of the coronavirus genomes that we sequenced, we encountered several major problems about the coronavirus sequences in GenBank as well as other coronavirus databases (Coronaviridae Bioinformatics Resource, http://athena.bioc.uvic.ca/database.php?db= coronaviridae; PATRIC http://patric.vbi.vt.edu) (25) . First, in GenBank, the non-structural proteins in the polyprotein encoded by orf1ab were not annotated. Second, in all databases, for the non-structural proteins encoded by ORFs downstream to orf1ab, the annotations are often confusing because they are not annotated using a standardized system. Third, multiple accession numbers are often present for reference sequences (26) . These problems often lead to confusion when sequence retrieval is performed. Fourth, coronaviruses, especially SARS-CoV, amplified from different specimens may contain the same genome or gene sequences. These sequences usually lead to redundant work when they are analyzed.