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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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Autores principales: Muhire, Brejnev Muhizi, Varsani, Arvind, Martin, Darren Patrick
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178126/
https://www.ncbi.nlm.nih.gov/pubmed/25259891
http://dx.doi.org/10.1371/journal.pone.0108277
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author Muhire, Brejnev Muhizi
Varsani, Arvind
Martin, Darren Patrick
author_facet Muhire, Brejnev Muhizi
Varsani, Arvind
Martin, Darren Patrick
author_sort Muhire, Brejnev Muhizi
collection PubMed
description 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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spelling pubmed-41781262014-10-02 SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation Muhire, Brejnev Muhizi Varsani, Arvind Martin, Darren Patrick PLoS One Research Article 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). Public Library of Science 2014-09-26 /pmc/articles/PMC4178126/ /pubmed/25259891 http://dx.doi.org/10.1371/journal.pone.0108277 Text en © 2014 Muhire et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited.
spellingShingle Research Article
Muhire, Brejnev Muhizi
Varsani, Arvind
Martin, Darren Patrick
SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation
title SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation
title_full SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation
title_fullStr SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation
title_full_unstemmed SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation
title_short SDT: A Virus Classification Tool Based on Pairwise Sequence Alignment and Identity Calculation
title_sort sdt: a virus classification tool based on pairwise sequence alignment and identity calculation
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178126/
https://www.ncbi.nlm.nih.gov/pubmed/25259891
http://dx.doi.org/10.1371/journal.pone.0108277
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