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Navigating Comparative Genomics with Bio2.0 and GIS

Explore the new world of comparative genomics with Bio2.0 and the Genomic Information System (GIS). Visualize gene alignments, explore protein interactions, and map transcriptional networks. Join the scientific community in revolutionizing genomic research.

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Navigating Comparative Genomics with Bio2.0 and GIS

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  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

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

  6. 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…

  7. 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

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

  9. Demo

  10. 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

  11. Acknowledgements

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