Making sense of Sequences: Comparative Genomics and the New GIS

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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

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Overview

• Another Genomic Revolution
• Bio 2.0 Navigate and Share the graph
• Bringing GIS to Comparative Genomics
• Future Directions

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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

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Searching for similar genes
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(No Transcript)
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Example ClustalW alignment
mammalian sulfatases first 110 residues of the
catalytic domain
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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

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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

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SilverMap Model
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Demo
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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

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Acknowledgements