Aequatus:An open-source homology browser

Thanki, Anil S., Soranzo, Nicola, Herrero, Javier, Haerty, Wilfried ORCID: https://orcid.org/0000-0003-0111-191X and Davey, Robert P. (2018) Aequatus:An open-source homology browser. GigaScience, 7 (11). pp. 1-8. ISSN 2047-217X

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Abstract

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. Findings: 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 Gene Seq To Family workflow.

Item Type: Article
Additional Information: Funding Information: This work was strategically funded by the Biotechnology and Biological Sciences Research Council (BBSRC)(BBS/E/T/000PR5885, BBS/E/T/000PR9817) and through a EU TransPlant grant (BBS/E/T/000GP006). GeneSeqToFamily and the EI Galaxy platform are funded through the BBSRC-supported EI National Capability in e-Infrastructure (BBS/E/T/000PR9814). Publisher Copyright: © 2018. Published by Oxford University Press.
Uncontrolled Keywords: alignment,gene family,homology,phylogeny,synteny,visualization,computer science applications,health informatics ,/dk/atira/pure/subjectarea/asjc/1700/1706
Faculty \ School: Faculty of Science > School of Biological Sciences
Related URLs:
Depositing User: LivePure Connector
Date Deposited: 15 Sep 2022 14:30
Last Modified: 23 Sep 2022 02:58
URI: https://ueaeprints.uea.ac.uk/id/eprint/88320
DOI: 10.1093/gigascience/giy128

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