Title: Parallel Genomic Sequence-Search on an Ad-Hoc Grid

Presenter: Dr. Wuchun Feng
    Department of Computer Science, Virginia Tech

Date and Time: Monday, December 4, 2006, 3:00-4:00PM

Abstract:
The Basic Local Alignment Search Tool (BLAST) allows bioinformaticists to characterize an unknown sequence by comparing it against a database of known sequences. The similarity between sequences enables biologists to detect evolutionary relationships and infer biological properties of the unknown sequence. mpiBLAST, our parallel BLAST, decreases the search time of a 300-kB query from two full days to under 10 minutes on a 128-processor cluster and allows larger query files to be compared. Consequently, we propose to compare the largest query available, the NT database, against the largest database available, the NT database. The end result will provide critical information to biologists, including evolutionary, structural, and functional relationships between every sequence and family in the NT database. However, because of the time complexity to accomplish the above task, we run mpiBLAST on GreenGene, an ad-hoc grid that was constructed from donated computational, network, and storage resources during SC2005.
Seminar Location: The seminars are held at:
    Virginia Tech, Corporate Research Center
    1880 Pratt Drive, Building XV
    Seminar Room 2018, Second Floor
    Directions: Map (PDF)

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