PAirwise Sequence Comparison (PASC) and Its Application in the Classification of Filoviruses
Open Access
- 19 August 2012
- Vol. 4 (8) , 1318-1327
- https://doi.org/10.3390/v4081318
Abstract
PAirwise Sequence Comparison (PASC) is a tool that uses genome sequence similarity to help with virus classification. The PASC tool at NCBI uses two methods: local alignment based on BLAST and global alignment based on Needleman-Wunsch algorithm. It works for complete genomes of viruses of several families/groups, and for the family of Filoviridae, it currently includes 52 complete genomes available in GenBank. It has been shown that BLAST-based alignment approach works better for filoviruses, and therefore is recommended for establishing taxon demarcation criteria. When more genome sequences with high divergence become available, these demarcations will most likely become more precise. The tool can compare new genome sequences of filoviruses with the ones already in the database, and propose their taxonomic classification.Keywords
This publication has 9 references indexed in Scilit:
- Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2012)Archiv für die gesamte Virusforschung, 2012
- Discovery of an Ebolavirus-Like Filovirus in EuropePLoS Pathogens, 2011
- Proposal for a revised taxonomy of the family Filoviridae: classification, names of taxa and viruses, and virus abbreviationsArchiv für die gesamte Virusforschung, 2010
- Classification of Myoviridae bacteriophages using protein sequence similarityBMC Microbiology, 2009
- Newly Discovered Ebola Virus Associated with Hemorrhagic Fever Outbreak in UgandaPLoS Pathogens, 2008
- Unifying classical and molecular taxonomic classification: analysis of the Podoviridae using BLASTP-based toolsResearch in Microbiology, 2008
- National Center for Biotechnology Information Viral Genomes ProjectJournal of Virology, 2004
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- A general method applicable to the search for similarities in the amino acid sequence of two proteinsJournal of Molecular Biology, 1970