PIs: Robert Kosara and Cynthia Gibas, UNC Charlotte
Genome comparison is a common bioinformatics analysis task, but a survey of the literature suggests that comparative genomic studies are done in an ad hoc, investigator-dependent, and non-reproducible fashion. Comparative genomics analysis questions can generally be formulated as set queries: what differentiates genome A from genome B, or from a broader group of its taxo- nomic neighbors? Such queries are laborious to construct from non-integrated data. We are developing a data warehouse-type database system optimized for comparative genomics, linked to an interactive workflow builder and query tools. The database stores sequence-linked biological data in a way that supports OLAP (On-Line Analytical Processing) and complex set-based queries. The workflow tool focuses on guiding the user through core comparative genomic operations, and serves as an interface for populating the data warehouse. An interactive query allows the user to construct questions about the data. Set-based as well as individual record results are presented to the user in a way that can be easily browsed and compared.