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Home | DTI | 2005–06 funded proposals | Nevin Dale Young, Elizabeth Shoop, Steve Cannon

Initiatives in Digital Technology: 2005–06 Funded Proposals

Nevin Dale Young, Elizabeth Shoop, Steve Cannon

Client-server tools for combining biological ontologies, genome sequence comparisons, and evolutionary data: Hundreds of genomes have been sequenced in the last ten years.

Hundreds of genomes have been sequenced in the last ten years. This flood of data has led to the development of many new kinds of analytical tools, including software for managing and navigating "gene ontologies" (GO; a heirarchical structured language to describe gene functions, roles, and cellular locations); software for aligning, visualizing, and analyzing related genome sequences; and software for analyzing evolutionary relationships among genes within a genome and among species. What is generally lacking, however, are meta-tools for combining disparate software and data. Such integrative tools will be critical for synthesizing genomic data and enabling higher-order questions in systems biology.

In collaboration with other researchers, we have developed software for navigating and visualizing gene ontologies (GoGet and GoView), for identifying and visualizing comparative genomic data (DiagHunter, OrthoParaMap, CVIT: Chromosome VIsualization Tool), and exploring evolutionary data (ATV: A Tree Viewer). Two of these, GoView, and ATV, are java applications that interact with databases. Additional third-party Java genome visualization software is available, Argo and Artemis.

We propose extending these applications (GoView, CVIT, Argo, ATV) and integrating them using Java JBoss middleware, resulting in software that can be used either separately to examine focused data sets, or in combination to select items within any of the programs for display in the other programs. This will enable a user to select a group of genes by functional annotation, by location in the genome, or by evolutionary relationship, and to view the genes in any of these contexts in the other applications: by functional relationships in GoView, by genomc location in Argo or CVIT, or by evolutionary relationship in ATV.