aequatus-vis, a plugin to visualise homologous gene families
TRANSCRIPT
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,
@anilthanki
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