Virus Classification by Pairwise Sequence Comparison (PASC)

Pairwise sequence comparison (PASC) is a molecular classification tool for viruses. It calculates the pairwise identities of virus sequences within a virus family and displays their distributions, and can help determine demarcations at different taxonomic levels such as strain, species, genus, and subfamily levels. PASC has many advantages over conventional virus classification methods. The tool has been successfully applied to several virus families, although it may not work well for virus families with highly diverse genome organization. The PASC tool at NCBI established distributions of identity for a number of virus families. A new virus sequence can be tested with this system within a few minutes to suggest the taxonomic position of the virus in a specific family. This system eliminates potential discrepancies in the results caused by different algorithms and/or different data used by the virology community. Data in the system can be updated automatically to reflect changes in virus taxonomy and additions of new virus sequences to the public database. The web interface of the tool makes it easy to navigate and perform analyses.