International Mammalian Genome Society

B2 An Integrated Workbench for the Visualization and Analysis of Genomic Feature Organization

Carol Bult^1,2, Kate Beard-Tisdale², Max Egenhofer², and Constance Holden². ¹The Jackson Laboratory, Bar Harbor, Maine 04609 and ²The University of Maine, Orono, Maine 04469, USA

One of the major challenges facing the genome informatics research community is to develop tools for the graphical representation of biologically significant features (genes, promoters, repeat units, etc.) that are identified in genomic sequence using computational and experimental methods. We have developed a prototype visualization and analysis workbench that allows researchers to query and test for the significance of the spatial organization of genome sequence features. The prototype, called the Genome Spatial Information System (GenoSIS), has been developed as part of an interdisciplinary collaboration between scientists from the geographic information sciences, spatial databases, and genome informatics communities. GenoSIS draws from the methods and concepts used by the geographic sciences community for identifying spatial patterns in geographic data and representing information over multiple scales of resolution and applies them to genome information "space." The system is designed to work with genome data from any organism. The prototyping phase of GenoSIS has focussed on three areas: 1) interactive symbolic representations of sequence feature maps, 2) contextual queries (as opposed to keyword queries), and 3) exploratory spatial data analysis of genome feature organization. The results from the initial prototyping phase for this project will be presented and discussed.

The GenoSIS project is supported by NSF DBI 9723873.