VIRULIGN: fast codon-correct alignment and annotation of viral genomes

SUMMARY: Virus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit of these applications critically depends on accurate and correctly annotated alignments of geneti...

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Autores principales: Libin, Pieter J K, Deforche, Koen, Abecasis, Ana B, Theys, Kristof
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Applications Notes
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6513156/
https://www.ncbi.nlm.nih.gov/pubmed/30295730
http://dx.doi.org/10.1093/bioinformatics/bty851
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author Libin, Pieter J K
Deforche, Koen
Abecasis, Ana B
Theys, Kristof
author_facet Libin, Pieter J K
Deforche, Koen
Abecasis, Ana B
Theys, Kristof
author_sort Libin, Pieter J K
collection PubMed
description SUMMARY: Virus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit of these applications critically depends on accurate and correctly annotated alignments of genetically heterogeneous data. VIRULIGN was built for fast codon-correct alignments of large datasets, with standardized and formalized genome annotation and various alignment export formats. AVAILABILITY AND IMPLEMENTATION: VIRULIGN is freely available at https://github.com/rega-cev/virulign as an open source software project. SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online.
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spelling pubmed-65131562019-05-20 VIRULIGN: fast codon-correct alignment and annotation of viral genomes Libin, Pieter J K Deforche, Koen Abecasis, Ana B Theys, Kristof Bioinformatics Applications Notes SUMMARY: Virus sequence data are an essential resource for reconstructing spatiotemporal dynamics of viral spread as well as to inform treatment and prevention strategies. However, the potential benefit of these applications critically depends on accurate and correctly annotated alignments of genetically heterogeneous data. VIRULIGN was built for fast codon-correct alignments of large datasets, with standardized and formalized genome annotation and various alignment export formats. AVAILABILITY AND IMPLEMENTATION: VIRULIGN is freely available at https://github.com/rega-cev/virulign as an open source software project. SUPPLEMENTARY INFORMATION: Supplementary data is available at Bioinformatics online. Oxford University Press 2019-05-15 2018-10-08 /pmc/articles/PMC6513156/ /pubmed/30295730 http://dx.doi.org/10.1093/bioinformatics/bty851 Text en © The Author(s) 2018. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Applications Notes
Libin, Pieter J K
Deforche, Koen
Abecasis, Ana B
Theys, Kristof
VIRULIGN: fast codon-correct alignment and annotation of viral genomes
title VIRULIGN: fast codon-correct alignment and annotation of viral genomes
title_full VIRULIGN: fast codon-correct alignment and annotation of viral genomes
title_fullStr VIRULIGN: fast codon-correct alignment and annotation of viral genomes
title_full_unstemmed VIRULIGN: fast codon-correct alignment and annotation of viral genomes
title_short VIRULIGN: fast codon-correct alignment and annotation of viral genomes
title_sort virulign: fast codon-correct alignment and annotation of viral genomes
topic Applications Notes
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6513156/
https://www.ncbi.nlm.nih.gov/pubmed/30295730
http://dx.doi.org/10.1093/bioinformatics/bty851
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