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PLoS One. 2014 Sep 26;9(9):e108277. doi: 10.1371/journal.pone.0108277. eCollection 2014.

SDT: a virus classification tool based on pairwise sequence alignment and identity calculation.

Author information

1
Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa.
2
Department of Clinical Laboratory Sciences, University of Cape Town, Cape Town, South Africa; School of Biological Sciences and Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand; Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, Gainesville, Florida, United States of America.

Abstract

The perpetually increasing rate at which viral full-genome sequences are being determined is creating a pressing demand for computational tools that will aid the objective classification of these genome sequences. Taxonomic classification approaches that are based on pairwise genetic identity measures are potentially highly automatable and are progressively gaining favour with the International Committee on Taxonomy of Viruses (ICTV). There are, however, various issues with the calculation of such measures that could potentially undermine the accuracy and consistency with which they can be applied to virus classification. Firstly, pairwise sequence identities computed based on multiple sequence alignments rather than on multiple independent pairwise alignments can lead to the deflation of identity scores with increasing dataset sizes. Also, when gap-characters need to be introduced during sequence alignments to account for insertions and deletions, methodological variations in the way that these characters are introduced and handled during pairwise genetic identity calculations can cause high degrees of inconsistency in the way that different methods classify the same sets of sequences. Here we present Sequence Demarcation Tool (SDT), a free user-friendly computer program that aims to provide a robust and highly reproducible means of objectively using pairwise genetic identity calculations to classify any set of nucleotide or amino acid sequences. SDT can produce publication quality pairwise identity plots and colour-coded distance matrices to further aid the classification of sequences according to ICTV approved taxonomic demarcation criteria. Besides a graphical interface version of the program for Windows computers, command-line versions of the program are available for a variety of different operating systems (including a parallel version for cluster computing platforms).

PMID:
25259891
PMCID:
PMC4178126
DOI:
10.1371/journal.pone.0108277
[Indexed for MEDLINE]
Free PMC Article

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