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Similar_Join: Extending DBMS with a Bio-specific Operator

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Similar_Join: Extending DBMS with a Bio-specific Operator
Existing sequence comparison software applications lack automation, abstraction, performance, and flexibility. Users need a new way of studying and applying sequence comparisons in the post-genomics era. We invented and developed a new bio-specific Database Management System perator, Similar_Join, to abstract the labor-intensive batch sequence similarity search task into a syntactically concise database operation. We implemented the Similar_Join operator as part of a relational operator package. This implementation enabled us to write simple PL/SQL scripts within the DBMS to accomplish routine sequence similarity searches conveniently, for example, a “batch BLAST” that compares 7,000 human genes against 500,000 human Expressed Sequence Tags (EST) in a few hours. We also implemented a simple version of Similar_Join as a database operator in the extended data cartridge of Oracle 8i object-relational DBMS. When fully integrated into SQL language extensions, we demonstrated this opera...
Jake Yue Chen, John V. Carlis
Added 05 Jul 2010
Updated 05 Jul 2010
Type Conference
Year 2003
Where SAC
Authors Jake Yue Chen, John V. Carlis
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