A minimum reporting standard for multiple sequence alignments

Multiple sequence alignments (MSAs) play a pivotal role in studies of molecular sequence data, but nobody has developed a minimum reporting standard (MRS) to quantify the completeness of MSAs in terms of completely specified nucleotides or amino acids. We present an MRS that relies on four simple co...

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Detalles Bibliográficos
Autores principales: Wong, Thomas K F, Kalyaanamoorthy, Subha, Meusemann, Karen, Yeates, David K, Misof, Bernhard, Jermiin, Lars S
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Methods Article
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671350/
https://www.ncbi.nlm.nih.gov/pubmed/33575581
http://dx.doi.org/10.1093/nargab/lqaa024
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author Wong, Thomas K F
Kalyaanamoorthy, Subha
Meusemann, Karen
Yeates, David K
Misof, Bernhard
Jermiin, Lars S
author_facet Wong, Thomas K F
Kalyaanamoorthy, Subha
Meusemann, Karen
Yeates, David K
Misof, Bernhard
Jermiin, Lars S
author_sort Wong, Thomas K F
collection PubMed
description Multiple sequence alignments (MSAs) play a pivotal role in studies of molecular sequence data, but nobody has developed a minimum reporting standard (MRS) to quantify the completeness of MSAs in terms of completely specified nucleotides or amino acids. We present an MRS that relies on four simple completeness metrics. The metrics are implemented in AliStat, a program developed to support the MRS. A survey of published MSAs illustrates the benefits and unprecedented transparency offered by the MRS.
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spelling pubmed-76713502021-02-10 A minimum reporting standard for multiple sequence alignments Wong, Thomas K F Kalyaanamoorthy, Subha Meusemann, Karen Yeates, David K Misof, Bernhard Jermiin, Lars S NAR Genom Bioinform Methods Article Multiple sequence alignments (MSAs) play a pivotal role in studies of molecular sequence data, but nobody has developed a minimum reporting standard (MRS) to quantify the completeness of MSAs in terms of completely specified nucleotides or amino acids. We present an MRS that relies on four simple completeness metrics. The metrics are implemented in AliStat, a program developed to support the MRS. A survey of published MSAs illustrates the benefits and unprecedented transparency offered by the MRS. Oxford University Press 2020-04-14 /pmc/articles/PMC7671350/ /pubmed/33575581 http://dx.doi.org/10.1093/nargab/lqaa024 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of NAR Genomics and Bioinformatics. 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 Methods Article
Wong, Thomas K F
Kalyaanamoorthy, Subha
Meusemann, Karen
Yeates, David K
Misof, Bernhard
Jermiin, Lars S
A minimum reporting standard for multiple sequence alignments
title A minimum reporting standard for multiple sequence alignments
title_full A minimum reporting standard for multiple sequence alignments
title_fullStr A minimum reporting standard for multiple sequence alignments
title_full_unstemmed A minimum reporting standard for multiple sequence alignments
title_short A minimum reporting standard for multiple sequence alignments
title_sort minimum reporting standard for multiple sequence alignments
topic Methods Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7671350/
https://www.ncbi.nlm.nih.gov/pubmed/33575581
http://dx.doi.org/10.1093/nargab/lqaa024
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