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.
Highlights
The family Filoviridae belongs to the order Mononegavirales
The results clearly indicate that (a) sequence-based classification agrees with the current International Committee on Taxonomy of Viruses (ICTV) taxonomy for the family
We believe the BLAST-based alignment result represents the true relationship among genome sequences of filoviruses, and should be used to establish taxa demarcation criteria, which are between 64% and 77%
Summary
The family Filoviridae belongs to the order Mononegavirales. Filovirus genomes are single-stranded, negative sense RNAs of about 19 kb, which encode 7 structural proteins. PAirwise Sequence Comparison (PASC) is a tool that can help virus classification using genome sequences [4]. It calculates the percent of pairwise sequence identity for all published complete genomes within a virus family/group, and plots the frequency distribution. In many virus families/groups, there are clear peaks in percent identity that represent pairs of viruses belonging to the same species, to different species but to the same genus, or to different genera. When these peaks are well separated, the identity percentage at their boundaries can serve as one of the species/genera demarcation criteria. We describe the application of PASC to the classification of filoviruses
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