Making sense of Sequences: Comparative Genomics and the New GIS

1. Making sense of Sequences: Comparative Genomics and the New GIS Xin-Yi Chua Peter Ansell, Chris Bowles, Lawrence Buckingham, James M. Hogan, Scott Mann, Paul Roe, Jiro Sumitomo, Jan M. Weinert www.mquter.qut.edu.au/bio

2. Overview Another Genomic Revolution Bio 2.0: Navigate and Share the graph Bringing ‘GIS’ to Comparative Genomics Future Directions

3. Another Genomic Revolution • An explosion in genomic data • The rise of population genomics & proteomics • Alignment does not scale to the new BioScience • Comparative genomics • Gene regulation • Protein characterisation

4. Searching for similar genes 3e-56 Results “Hits” BLAST 5e-56 Reference gene 9e -45 … 9.9

6. Example ClustalW alignment mammalian sulfatases: first 110 residues of the catalytic domain

7. Bio2.0: Navigate & Share the Graph • We allow scientists to visualise the graph • Make the topology fit the question • Visualisation is navigation • Let the graph answer the question • Refine and test hypotheses • And then make the answer available • Peer communities & link-based publication • Sharing the vision…

8. Bringing ‘GIS’ to Comparative Genomics • The new ‘GIS’ – Genomic Information System • All about distances and what works for the user • Linking to data sources via Bio2RDF • Combining a collection of data sources together • Exploiting tags and ontologies

9. SilverMap Model Tags Bio2RDF Bio2RDF TRN SilverMap Blastcomponent BlastDB Protein-protein interactions User defined distance measures

10. Demo

11. Future directions • Future applications • Support user defined distances • Transcriptional Regulatory Network analyses • Protein-Protein interactions • Bringing our tools to the community • Making SilverMap the lingua franca of genomic publication • The lab wiki and public web site • Integration, tagging and sharing of views

12. Acknowledgements