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aequatus-vis
AnilThanki
Scientific Programmer –TGAC, UK
@anilthanki @aequatus
RECAP
Aequatus
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
@anilthanki
Aequatus
@anilthanki
monoamine oxidase
Aequatus
Homologous Genes with shared exon information
@anilthanki
monoamine oxidase
Aequatus
GeneTree
@anilthanki
monoamine oxidase
Aequatus
Reference information
Controls
@anilthanki
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
@anilthanki
aequatus-vis
1. GeneTree
• JSON / Newick
2. Gene structural Info
• JSON
@anilthanki
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
@anilthanki
Example of visualising homologous genes in Aequatus using aequauts-vis
Next
update
Aequatus e! Rest API
@anilthanki
Example of visualising homologous genes fetched from e! Rest API in Aequatus using aequatus-vis
Testing
Galaxy
@anilthanki
Example of visualising homologous genes in Galaxy using aequatus-vis
Pull request
TGAC
Robert Davey
Sarah Ayling
Nicola Soranzo
http://aequatus.tgac.ac.uk
@anilthanki and @aequatus
Contact
Acknowledgements
@anilthanki
Javier Herrero
UCL Cancer Institute, UK
Matthieu Muffato
EBI-EMBL, UK
Thank you
■ Questions?
■ Suggestions?
■ Advice?
■ Potential Users / collaborators ?
@anilthanki

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Aequatus-vis, a plugin to visualise homologous gene families

Editor's Notes

  1. Why Aequatus? Info e!
  2. Why Aequatus? Info e!
  3. Strand information… Purpose .. Succesfull example Compare with e! Compara tree
  4. Poster number