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Aequatus: An open-source homology browser

View ORCID ProfileAnil S. Thanki, View ORCID ProfileNicola Soranzo, View ORCID ProfileJavier Herrero, View ORCID ProfileWilfried Haerty, View ORCID ProfileRobert P. Davey
doi: https://doi.org/10.1101/055632
Anil S. Thanki
1Earlham Institute, Norwich, NR4 7UZ, UK
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Nicola Soranzo
1Earlham Institute, Norwich, NR4 7UZ, UK
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Javier Herrero
1Earlham Institute, Norwich, NR4 7UZ, UK
2Bill Lyons Informatics Centre, UCL Cancer Institute, London WC1E 6DD, UK
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Wilfried Haerty
1Earlham Institute, Norwich, NR4 7UZ, UK
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Robert P. Davey
1Earlham Institute, Norwich, NR4 7UZ, UK
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Abstract

Background 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 characterisation enables the identification of syntenic blocks, which can then be visualised 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, a standalone web-based tool that provides an in-depth view of gene structure across gene families, with various options to render and filter visualisations. It relies on pre-calculated 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 fulfils the visualisation aspects of Aequatus, available within the Galaxy web platform as a visualisation plugin, which can be used to visualise gene trees generated by the GeneSeqToFamily workflow.

Availability Aequatus is an open-source tool freely available to download under the MIT license at https://github.com/TGAC/Aequatus. A demo server is available at http://aequatus.earlham.ac.uk/. A publicly available instance of the GeneSeqToFamily workflow to generate gene tree information and visualise it using Aequatus is available on the Galaxy EU server at https://usegalaxy.eu.

Contacts Anil.Thanki{at}earlham.ac.uk and Robert.Davey{at}earlham.ac.uk

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted June 15, 2018.
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Aequatus: An open-source homology browser
Anil S. Thanki, Nicola Soranzo, Javier Herrero, Wilfried Haerty, Robert P. Davey
bioRxiv 055632; doi: https://doi.org/10.1101/055632
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Aequatus: An open-source homology browser
Anil S. Thanki, Nicola Soranzo, Javier Herrero, Wilfried Haerty, Robert P. Davey
bioRxiv 055632; doi: https://doi.org/10.1101/055632

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