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Impact of alignment algorithm on the estimation of pairwise genetic similarity of porcine reproductive and respiratory syndrome virus (PRRSV)

BACKGROUND: Porcine reproductive and respiratory syndrome (PRRS) is a major threat to the swine industry. It is caused by the PRRS virus (PRRSV). Determination and comparison of the nucleotide sequences of PRRSV strains provides useful information in support of control initiatives or epidemiological...

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Autores principales: Lambert, Marie-Ève, Arsenault, Julie, Delisle, Benjamin, Audet, Pascal, Poljak, Zvonimir, D’Allaire, Sylvie
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6505299/
https://www.ncbi.nlm.nih.gov/pubmed/31068211
http://dx.doi.org/10.1186/s12917-019-1890-0
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author Lambert, Marie-Ève
Arsenault, Julie
Delisle, Benjamin
Audet, Pascal
Poljak, Zvonimir
D’Allaire, Sylvie
author_facet Lambert, Marie-Ève
Arsenault, Julie
Delisle, Benjamin
Audet, Pascal
Poljak, Zvonimir
D’Allaire, Sylvie
author_sort Lambert, Marie-Ève
collection PubMed
description BACKGROUND: Porcine reproductive and respiratory syndrome (PRRS) is a major threat to the swine industry. It is caused by the PRRS virus (PRRSV). Determination and comparison of the nucleotide sequences of PRRSV strains provides useful information in support of control initiatives or epidemiological studies on transmission patterns. The alignment of sequences is the first step in analyzing sequence data, with multiple algorithms being available, but little is known on the impact of this methodological choice. Here, a study was conducted to evaluate the impact of different alignment algorithms on the resulting aligned sequence dataset and on practical issues when applied to a large field database of PRRSV open reading frame (ORF) 5 sequences collected in Quebec, Canada, from 2010 to 2014. Five multiple sequence alignment programs were compared: Clustal W, Clustal Omega, Muscle, T-Coffee and MAFFT. RESULTS: The resulting alignments showed very similar results in terms of average pairwise genetic similarity, proportion of pairwise comparisons having ≥97.5% genetic similarity and sum of pairs (SP) score, except for T-Coffee where increased length of aligned datasets as well as limitation to handle large datasets were observed. CONCLUSIONS: Based on efficiency at minimizing the number of gaps in different dataset sizes with default open gap values as well as the capability to handle a large number of sequences in a timely manner, the use of Clustal Omega might be recommended for the management of PRRSV extensive database for both research and surveillance purposes.
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spelling pubmed-65052992019-05-10 Impact of alignment algorithm on the estimation of pairwise genetic similarity of porcine reproductive and respiratory syndrome virus (PRRSV) Lambert, Marie-Ève Arsenault, Julie Delisle, Benjamin Audet, Pascal Poljak, Zvonimir D’Allaire, Sylvie BMC Vet Res Research Article BACKGROUND: Porcine reproductive and respiratory syndrome (PRRS) is a major threat to the swine industry. It is caused by the PRRS virus (PRRSV). Determination and comparison of the nucleotide sequences of PRRSV strains provides useful information in support of control initiatives or epidemiological studies on transmission patterns. The alignment of sequences is the first step in analyzing sequence data, with multiple algorithms being available, but little is known on the impact of this methodological choice. Here, a study was conducted to evaluate the impact of different alignment algorithms on the resulting aligned sequence dataset and on practical issues when applied to a large field database of PRRSV open reading frame (ORF) 5 sequences collected in Quebec, Canada, from 2010 to 2014. Five multiple sequence alignment programs were compared: Clustal W, Clustal Omega, Muscle, T-Coffee and MAFFT. RESULTS: The resulting alignments showed very similar results in terms of average pairwise genetic similarity, proportion of pairwise comparisons having ≥97.5% genetic similarity and sum of pairs (SP) score, except for T-Coffee where increased length of aligned datasets as well as limitation to handle large datasets were observed. CONCLUSIONS: Based on efficiency at minimizing the number of gaps in different dataset sizes with default open gap values as well as the capability to handle a large number of sequences in a timely manner, the use of Clustal Omega might be recommended for the management of PRRSV extensive database for both research and surveillance purposes. BioMed Central 2019-05-08 /pmc/articles/PMC6505299/ /pubmed/31068211 http://dx.doi.org/10.1186/s12917-019-1890-0 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Research Article
Lambert, Marie-Ève
Arsenault, Julie
Delisle, Benjamin
Audet, Pascal
Poljak, Zvonimir
D’Allaire, Sylvie
Impact of alignment algorithm on the estimation of pairwise genetic similarity of porcine reproductive and respiratory syndrome virus (PRRSV)
title Impact of alignment algorithm on the estimation of pairwise genetic similarity of porcine reproductive and respiratory syndrome virus (PRRSV)
title_full Impact of alignment algorithm on the estimation of pairwise genetic similarity of porcine reproductive and respiratory syndrome virus (PRRSV)
title_fullStr Impact of alignment algorithm on the estimation of pairwise genetic similarity of porcine reproductive and respiratory syndrome virus (PRRSV)
title_full_unstemmed Impact of alignment algorithm on the estimation of pairwise genetic similarity of porcine reproductive and respiratory syndrome virus (PRRSV)
title_short Impact of alignment algorithm on the estimation of pairwise genetic similarity of porcine reproductive and respiratory syndrome virus (PRRSV)
title_sort impact of alignment algorithm on the estimation of pairwise genetic similarity of porcine reproductive and respiratory syndrome virus (prrsv)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6505299/
https://www.ncbi.nlm.nih.gov/pubmed/31068211
http://dx.doi.org/10.1186/s12917-019-1890-0
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