Anil K Thanki's talk at #ICG13 on Aequatus: An open-source homology browser. Presented at the GigaScience prize track, Shenzhen 26th October 2018

1. Aequatus: An open-source
homology browser
ANIL THANKI
Data Infrastructure and Algorithms
@anilthanki

2. www.earlham.ac.uk
Co-authors
Robert Davey
Earlham Institute
Nicola Soranzo
Earlham Institute
Wilfried Haerty
Earlham Institute
Javier Herrero
University College
London
Acknowledgements

3. Homology

4. www.earlham.ac.uk
Homology
• Homology is existence of shared ancestry between a pair of structures
in different species.
–i.e. genes
• The phylogenetic information inferred from the study of homologous
genes
–helps us to understand the evolution of gene families.

5. www.earlham.ac.uk
Homology
• Various tools available to visualise homology
–Ensembl
–Genomicus
–SynChro
• They provide an overview of phylogeny and/or syntenic regions
evolution at the family level
• They can not provide information about structural changes within a
gene

6. www.earlham.ac.uk
Homology - Tool example
Genomicus

7. www.earlham.ac.uk
Homology - Tool example
Map view Street view
Genomicus

8. Aequatus
http://aequatus.earlham.ac.uk/

9. www.earlham.ac.uk
Aequatus
• New open-source tool for visualisation of homologous genes
• Reads data directly from Ensembl Compara and Ensembl Core
Databases
• Three main views
1. Gene tree view
2. Sankey view
3. Tabular view

10. www.earlham.ac.uk
Aequatus - Gene tree view
• Phylogeny on left
• Detailed view of gene structure across gene families
• Shared exons use the same colour in each representation
• Also visualises Insertions and Deletions

11. www.earlham.ac.uk
Aequatus - Gene tree view
• Depicts the type of interrelation events that gave rise to the family:
–speciation, duplication, and gene splits

12. www.earlham.ac.uk
• 1-to-1 alignments between homologous genes are important for
pairwise comparison
• On the top (A): alignment on gene structure
• On the bottom (B): pairwise sequence alignments
Aequatus - Gene tree view

13. www.earlham.ac.uk
Aequatus - Gene tree view
• An interactive visualisation of the protein domains.
• Connects to SMART web server via REST API and queries for domains,
motifs, internal repeats, etc.
• Can be filtered and sorted based on E-value and source.
• Can be exported in CSV or Excel file format.

14. www.earlham.ac.uk
Aequatus - Gene tree view
• An interactive visualisation of the protein domains.

15. www.earlham.ac.uk
Aequatus - Sankey view
• Visualises homology as an interactive Sankey diagram
• Homologues of a selected gene are distinguished by homology type
–paralogs, 1-to-1 orthologs, 1-to-many orthologs
• Coloured by species
• Additional details for the homologous in the info panel on the right-
hand side.

16. www.earlham.ac.uk
Aequatus - Sankey view
• Visualises homology as an interactive Sankey diagram

17. www.earlham.ac.uk
Aequatus - Tabular view
• Visualises homology as an interactive table
• Contains statistical information for the homologous relationships.
• Allows the user to
–search for any homolog using a search box
–filter results for the type of homology or one or more species
• Export from the tabular view as Excel, CSV or PDF.

18. www.earlham.ac.uk
Aequatus - Tabular view
D = Filter based on Species
E = Filter based on Type of homology
A = Search Box
B = Detailed statistical information
C = Detailed pairwise alignment

19. Aequatus.js

20. www.earlham.ac.uk
Aequatus.js
• Aequatus.js is a JavaScript library based on the standalone Aequatus
software package
• It preserves interactive functionality of Aequatus
• Does not require Ensembl databases for data
• It has an ability to integration with countless web based applications
• Gene Tree
–JSON / Newick
• Gene structural info
–JSON
Input

21. Aequatus.js
Use Case
Galaxy and GeneSeqToFamily

22. www.earlham.ac.uk
Galaxy and GeneSeqToFamily
• Galaxy is an open source, web-based platform for data intensive
biomedical research.
• Aequatus.js plugin configured to be used into Galaxy
–available on GitHub and integrated into usegalaxy.eu
• Can visualises results of GeneSeqToFamily workflow
–a Galaxy workflow to find gene families based on the Ensembl
Compara GeneTrees pipeline
–https://doi.org/10.1093/gigascience/giy005

23. www.earlham.ac.uk
Galaxy and GeneSeqToFamily
Aequatus.js plugin in Galaxy

24. New stuff...

25. www.earlham.ac.uk
New stuff...
• The main extension to the Aequatus is incorporation of Ensembl REST
API.
• Aequatus can also retrieve latest data directly from Ensembl Compara
and Core databases held at the EMBL-EBI,
– without any need for local databases
– avoids the need for local storage space
– improves the portability of Aequatus

26. www.earlham.ac.uk
New stuff...
• The main extension to the Aequatus is incorporation of Ensembl REST
API.

27. www.earlham.ac.uk
New stuff...
• The main extension to the Aequatus is incorporation of Ensembl REST
API.

28. www.earlham.ac.uk
• Thanki AS, Soranzo N, Haerty W, Herrero J, Davey RP. Aequatus:
An open-source homology browser. GigaScience 2018
• Demo:
– Demo: http://aequatus.earlham.ac.uk/
• Source Code:
– GitHub: https://github.com/TGAC/Aequatus
• Aequatus.js plugin
– GitHub: https://github.com/TGAC/aequatus.js
• E-mail: Anil.Thanki@earlham.ac.uk
• Twitter: @anilthanki
Thank You..
Questions…?