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- This project was initiated upon a request from Dr. Claude Fauquet, Danforth Plant Science Center.
- Briefly, pairwise global alignment will be performed on all complete genomes
for each viral families, and their percentage of identities calculated. The number of pairs at each percentages is plotted, and this distribution will form distinguished peaks for viruses at isolate, species, genus, and subfamily levels.
- The percentage range of each peak serves as a good reference for taxonomy classification based on sequence similarities.
- This procedure has been applied successfully on geminiviruses, potyviruses, flexiviruses and papillomaviruses, and it is our intent to use it as a standard tool and expand it to all viral families for which the system is applicable. Once established for one family, this tool will assist users to correctly classify new viruses and consequently name new viruses they have sequenced accordingly.
- The distributions will be updated regularly to reflect the most current distribution and to include new isolates and species approved by ICTV.
How to cite PASC:
- Bao Y., Kapustin Y. & Tatusova T. (2008). Virus Classification by Pairwise Sequence Comparison (PASC). Encyclopedia of Virology, 5 vols. (B.W.J. Mahy and M.H.V. Van Regenmortel, Editors). Oxford: Elsevier. Vol. 5, 342-348.
Other references:
- Adams M.J., Antoniw J.F., Bar-Joseph M., Brunt A.A., Candresse T., Foster G.D., Martelli G.P., Milne R.G., Zavriev S.K. and Fauquet C.M. (2004). The new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation. Archives of Virology 149, 1045-1060.
- Adams M.J., Antoniw J.F. and Fauquet C.M. (2005). Molecular criteria for genus and species discrimination within the family Potyviridae. Archives of Virology 150,459-479.
- de Villiers E.M., Fauquet C., Broker T.R., Bernard H.U. and zur Hausen H. (2004). Classification of papillomaviruses. Virology 324, 17-27.
- Fauquet, C.M. and Stanley, J. (2003). Geminivirus classification and nomenclature: progress and problems. Annals of Applied Biology 142, 165-189.
- Oberste, M.S., Maher, K, Kilpatrick, D.R and Pallansch, M.A. (1999). Molecular Evolution of the Human Enteroviruses: Correlation of serotype with VP1 sequence and application to picornavirus classification. Journal of Virology 73, 1941–1948.
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