Periscope/SQ: interactive exploration of biological sequence databases

Authors:
Sandeep Tata;Willis Lang;Jignesh M. Patel
Affiliations:
University of Michigan, Ann Arbor, Michigan;University of Michigan, Ann Arbor, Michigan;University of Michigan, Ann Arbor, Michigan
Venue:
VLDB '07 Proceedings of the 33rd international conference on Very large data bases
Year:
2007

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Abstract

Life science laboratories today have to rely on procedural techniques to store and manage large sequence datasets. Procedural techniques are cumbersome to use and are often very inefficient compared to optimized declarative techniques. We have designed and implemented a system called Periscope/SQ that makes it possible to rapidly express complex queries within a declarative framework and take advantage of database-style query optimization. As a result, queries in Periscope/SQ run orders of magnitude faster than typical procedural implementations. We demonstrate the power of Persicope/SQ through an application called Gene-Locator which allows biologists to rapidly explore large genomic sequence databases.