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Viruses. 2012 Aug;4(8):1318-27. Epub 2012 Aug 20.

PAirwise Sequence Comparison (PASC) and its application in the classification of filoviruses.

Author information

1
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20892, USA. bao@ncbi.nlm.nih.gov

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 demarcations criteria. When more genome sequences with high divergence become available, these demarcation 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:

Filoviridae; ICTV; International Committee on Taxonomy of Viruses; NCBI; National Center for Biotechnology Information; PASC; PAirwise Sequence Comparison; filovirus; virus classification; virus taxonomy

PMID:
23012628
PMCID:
PMC3446765
DOI:
10.3390/v4081318
[Indexed for MEDLINE]
Free PMC Article
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