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Anil Thanki at #ICG13: Aequatus: An open-source homology browser

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

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Anil Thanki at #ICG13: Aequatus: An open-source homology browser

  1. 1. Aequatus: An open-source homology browser ANIL THANKI Data Infrastructure and Algorithms @anilthanki
  2. 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. 3. Homology
  4. 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. 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. 6. www.earlham.ac.uk Homology - Tool example Genomicus
  7. 7. www.earlham.ac.uk Homology - Tool example Map view Street view Genomicus
  8. 8. Aequatus http://aequatus.earlham.ac.uk/
  9. 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. 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. 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. 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. 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. 14. www.earlham.ac.uk Aequatus - Gene tree view • An interactive visualisation of the protein domains.
  15. 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. 16. www.earlham.ac.uk Aequatus - Sankey view • Visualises homology as an interactive Sankey diagram
  17. 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. 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. 19. Aequatus.js
  20. 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. 21. Aequatus.js Use Case Galaxy and GeneSeqToFamily
  22. 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. 23. www.earlham.ac.uk Galaxy and GeneSeqToFamily Aequatus.js plugin in Galaxy
  24. 24. New stuff...
  25. 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. 26. www.earlham.ac.uk New stuff... • The main extension to the Aequatus is incorporation of Ensembl REST API.
  27. 27. www.earlham.ac.uk New stuff... • The main extension to the Aequatus is incorporation of Ensembl REST API.
  28. 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…?

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