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

 

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dc.contributor.author Muhire, Brejnev Muhizi
dc.contributor.author Varsani, Arvind
dc.contributor.author Martin, Darren Patrick
dc.date.accessioned 2016-08-15T12:24:31Z
dc.date.available 2016-08-15T12:24:31Z
dc.date.issued 2014
dc.identifier http://dx.doi.org/ 10.1371/journal.pone.0108277
dc.identifier.citation Muhire, B. M., Varsani, A., & Martin, D. P. (2014). SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PloS one, 9(9), e108277. en_ZA
dc.identifier.issn 1932-6203 en_ZA
dc.identifier.uri http://hdl.handle.net/11427/21242
dc.description.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). en_ZA
dc.language eng en_ZA
dc.publisher Public Library of Science en_ZA
dc.rights Creative Commons Attribution 4.0 International (CC BY 4.0) *
dc.rights.uri http://creativecommons.org/licenses/by/4.0/ en_ZA
dc.source PLoS ONE en_ZA
dc.source.uri http://journals.plos.org/plosone/
dc.title SDT: a virus classification tool based on pairwise sequence alignment and identity calculation en_ZA
dc.type Journal Article en_ZA
dc.date.updated 2016-08-12T13:44:43Z
uct.type.publication Research en_ZA
uct.type.resource Article en_ZA
dc.publisher.institution University of Cape Town
dc.publisher.faculty Faculty of Health Sciences en_ZA
dc.publisher.department Department of Clinical Laboratory Sciences en_ZA
uct.type.filetype Text
uct.type.filetype Image
dc.identifier.apacitation Muhire, B. M., Varsani, A., & Martin, D. P. (2014). SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. <i>PLoS ONE</i>, http://hdl.handle.net/11427/21242 en_ZA
dc.identifier.chicagocitation Muhire, Brejnev Muhizi, Arvind Varsani, and Darren Patrick Martin "SDT: a virus classification tool based on pairwise sequence alignment and identity calculation." <i>PLoS ONE</i> (2014) http://hdl.handle.net/11427/21242 en_ZA
dc.identifier.vancouvercitation Muhire BM, Varsani A, Martin DP. SDT: a virus classification tool based on pairwise sequence alignment and identity calculation. PLoS ONE. 2014; http://hdl.handle.net/11427/21242. en_ZA
dc.identifier.ris TY - Journal Article AU - Muhire, Brejnev Muhizi AU - Varsani, Arvind AU - Martin, Darren Patrick AB - 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). DA - 2014 DB - OpenUCT DP - University of Cape Town J1 - PLoS ONE LK - https://open.uct.ac.za PB - University of Cape Town PY - 2014 SM - 1932-6203 T1 - SDT: a virus classification tool based on pairwise sequence alignment and identity calculation TI - SDT: a virus classification tool based on pairwise sequence alignment and identity calculation UR - http://hdl.handle.net/11427/21242 ER - en_ZA


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