Aequatus: an open-source homology browser

Phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of genes and gene families, including the identification of ancestral gene duplication events as well as regions under positive or purifying selection within lineages. Gene family and orthogroup characterization enables the identification of syntenic blocks, which can then be visualized with various tools. Unfortunately, currently available tools display only an overview of syntenic regions as a whole, limited to the gene level, and none provide further details about structural changes within genes, such as the conservation of ancestral exon boundaries amongst multiple genomes. We present Aequatus, an open-source web-based tool that provides an in-depth view of gene structure across gene families, with various options to render and filter visualizations. It relies on precalculated alignment and gene feature information typically held in, but not limited to, the Ensembl Compara and Core databases. We also offer Aequatus.js, a reusable JavaScript module that fulfills the visualization aspects of Aequatus, available within the Galaxy web platform as a visualization plug-in, which can be used to visualize gene trees generated by the GeneSeqToFamily workflow.

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Additional Info

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Author Thanki, Anil S
Last Updated November 20, 2019, 16:49 (UTC)
Created August 1, 2019, 10:28 (UTC)
Article Host Type publisher
Article Is Open Access true
Article License Type cc-by
Article Version Type publishedVersion
Citation Report https://scite.ai/reports/10.1093/gigascience/giy128
DOI 10.1093/gigascience/giy128
Date Last Updated 2019-07-24T12:35:11.952736
Evidence open (via page says license)
Funder code(s) Biotechnology and Biological Sciences Research Council (BBS/E/T/000PR5885, BBS/E/T/000GP006, BBS/E/T/000PR9817, BBS/E/T/000PR9814)
Journal Is Open Access true
Open Access Status gold
PDF URL https://academic.oup.com/gigascience/article-pdf/7/11/giy128/26731255/giy128.pdf
Publisher URL https://doi.org/10.1093/gigascience/giy128