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

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 measur...

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Vydané v:PloS one Ročník 9; číslo 9; s. e108277
Hlavní autori: Muhire, Brejnev Muhizi, Varsani, Arvind, Martin, Darren Patrick
Médium: Journal Article
Jazyk:English
Vydavateľské údaje: United States Public Library of Science 26.09.2014
Public Library of Science (PLoS)
Predmet:
Alcea rosea
Alignment
Amino acids
Base Sequence
Biology and Life Sciences
Classification
Computational Biology - methods
Computer applications
Computer viruses
Deoxyribonucleic acid
DNA
Gene sequencing
Genomes
Laboratories
Mathematical analysis
Nucleotide sequence
Operating systems
Phylogenetics
Sequence Alignment
Software
Taxonomy
Viruses
Viruses - classification
Viruses - genetics
Windows (computer programs)
South Africa
Antarctica
United States > US
China
ISSN:1932-6203, 1932-6203
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Popis
Shrnutí: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).
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Conceived and designed the experiments: BMM DPM AV. Performed the experiments: BMM DPM. Analyzed the data: BMM DPM. Contributed reagents/materials/analysis tools: BMM DPM. Contributed to the writing of the manuscript: BMM AV DPM. Software design and programming: BMM.
Competing Interests: The authors have declared that no competing interests exist.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0108277