By Topic

Parallel Genomic Sequence-Searching on an Ad-Hoc Grid: Experiences, Lessons Learned, and Implications

Sign In

Cookies must be enabled to login.After enabling cookies , please use refresh or reload or ctrl+f5 on the browser for the login options.

Formats Non-Member Member
$31 $13
Learn how you can qualify for the best price for this item!
Become an IEEE Member or Subscribe to
IEEE Xplore for exclusive pricing!
close button

puzzle piece

IEEE membership options for an individual and IEEE Xplore subscriptions for an organization offer the most affordable access to essential journal articles, conference papers, standards, eBooks, and eLearning courses.

Learn more about:

IEEE membership

IEEE Xplore subscriptions

5 Author(s)

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 on the current NT database from over 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 entire NT database, against the largest database available, the entire NT database. The result of this comparison can provide critical information to the biology community, including insightful evolutionary, structural, and functional relationships between every sequence and family in the NT database. Preliminary projections indicated that to complete the task in a reasonable length of time required more processors than were available to us at a single site. Hence, we assembled GreenGene, an ad-hoc grid that was constructed "on the fly" from donated computational, network, and storage resources during last year's SC|05. GreenGene consisted of 3048 processors from machines that were distributed across the United States. This paper presents a case study of mpiBLAST on GreenGene - specifically, a pre-run characterization of the computation, the hardware and software architectural design, experimental results, and future directions

Published in:

SC 2006 Conference, Proceedings of the ACM/IEEE

Date of Conference:

11-17 Nov. 2006