aequatus-visAnil Thanki

Scientific Programmer – TGAC, UK@anilthanki @aequatus

RECAPAequatus

Homology and Phylogeny

■ Homology is existence of shared ancestry between a pair of structures, or genes, in different species.

■ The phylogenetic information inferred from the study of homologous genes helps us to understand the evolution of gene families,

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Aequatus

■ Aequatus is an open-source web based tool to visualise homologous genes with phylogenetic tree.

■ Aequatus reads data directly from Ensembl Compara and Ensembl Core Databases

■ http://aequatus.tgac.ac.uk ■ GitHub: https://github.com/TGAC/Aequatus-Browser

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Aequatus

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monoamine oxidase

Aequatus

Homologous Genes with shared exon information

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monoamine oxidase

Aequatus

Gene Tree

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monoamine oxidase

Aequatus

Reference information

Controls

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monoamine oxidase

Reference information

Aequatus

@anilthanki

• Aequatus visualises similarity amongst homologous genes along with the event type responsible for existence of the gene, • for example speciation, duplication, gene-split etc.

• Also indicates insertions and deletions• With user-friendly interactions and viewing options

monoamine oxidase

aequatus-vis

aequatus-vis■ aequatus-vis is a JavaScript plugin to visualise homologous genes

through alignment and phylogeny information. ■ It preserves interactive functionality of Aequatus ■ It has an ability to integration with countless web based applications

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aequatus-vis

1. Gene Tree • JSON / Newick

2. Gene structural Info• JSON

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JSON format returned from e! server

■ aequatus-vis takes gene tree and gene structural information as input

■ Gene tree in either Newick or JSON from e! server■ Gene structures in JSON format from e! server

EXAMPLES

Aequatus

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Example of visualising homologous genes in Aequatus using aequauts-vis

Next update

Aequatus e! Rest API

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Example of visualising homologous genes fetched from e! Rest API in Aequatus using aequatus-vis

Testing

Galaxy

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Example of visualising homologous genes in Galaxy using aequatus-vis

Pull request

TGAC

Robert DaveySarah AylingNicola Soranzo

http://aequatus.tgac.ac.uk

@anilthanki and @aequatus

Contact

Acknowledgements

@anilthanki

Javier HerreroUCL Cancer Institute, UK

Matthieu Muffato EBI-EMBL, UK

Thank you

■ Questions?■ Suggestions?■ Advice?■ Potential Users / collaborators ?

@anilthanki