pairwise sequence comparison (pasc) and its application in the classification of filoviruses成对序列比较(pasc)丝状病毒的分类及其应用.pdfVIP

Viruses 2012, 4, 1318-1327; doi:10.3390/v4081318 OPEN ACCESS viruses ISSN 1999-4915 /journal/viruses Article PAirwise Sequence Comparison (PASC) and Its Application in the Classification of Filoviruses Yiming Bao *, Vyacheslav Chetvernin and Tatiana Tatusova National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20892, USA; E-Mails: chetvern@ (V.C.); tatiana@ (T.T.) * Author to whom correspondence should be addressed; E-Mail: bao@ (Y.B.); Tel.: +1-301-435-5939; Fax: +1-301-402-9651. Received: 3 July 2012; in revised form : 16 August 2012 / Accepted: 16 August 2012 / Published: 20 August 2012 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 databas