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AlignStat: a web-tool and R package for statistical comparison of alternative multiple sequence alignments

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journal contribution
posted on 20.01.2021, 08:31 by Thomas ShafeeThomas Shafee, Ira Cooke
© 2016 The Author(s). Background: Alternative sequence alignment algorithms yield different results. It is therefore useful to quantify the similarities and differences between alternative alignments of the same sequences. These measurements can identify regions of consensus that are likely to be most informative in downstream analysis. They can also highlight systematic differences between alignments that relate to differences in the alignment algorithms themselves. Results: Here we present a simple method for aligning two alternative multiple sequence alignments to one another and assessing their similarity. Differences are categorised into merges, splits or shifts in one alignment relative to the other. A set of graphical visualisations allow for intuitive interpretation of the data. Conclusions: AlignStat enables the easy one-off online use of MSA similarity comparisons or into R pipelines. The web-tool is available at AlignStat.Science.LaTrobe.edu.au. The R package, readme and example data are available on CRAN and GitHub.com/TS404/AlignStat.

Funding

TS was supported by the Australian Research Council. IC was supported by the Victorian Life Sciences Computation Initiative, a collaboration between Melbourne, Monash and La Trobe Universities and an initiative of the Victorian Government, Australia. The funding bodies had no further roles.

Australian Research Council

Victorian Life Sciences Computation Initiative

Victorian Government, Australia

History

Publication Date

01/01/2016

Journal

BMC Bioinformatics

Volume

17

Issue

1

Article Number

434

Pagination

6p. (p. 1-6)

Publisher

BioMed Central

ISSN

1471-2105

Rights Statement

The Author reserves all moral rights over the deposited text and must be credited if any re-use occurs. Documents deposited in OPAL are the Open Access versions of outputs published elsewhere. Changes resulting from the publishing process may therefore not be reflected in this document. The final published version may be obtained via the publisher’s DOI. Please note that additional copyright and access restrictions may apply to the published version.