DocumentCode
3039760
Title
Whole Genome Comparison on a Network of Workstations
Author
Jacob, Arpith ; Sanyal, Sugata ; Paprzycki, Marcin ; Arora, Rajan ; Ganzha, Maria
Author_Institution
Vellore Inst. of Technol., Vellore
fYear
2007
fDate
5-8 July 2007
Firstpage
7
Lastpage
7
Abstract
Whole genome comparison consists of comparing or aligning genome sequences with a goal of finding similarities between them. Previously we have shown how SIMD extensions used in Intel processors can be used to efficiently implement the, genome comparing, Smith-Waterman algorithm. Here we present distributed version of that algorithm. We show that on somewhat outdated hardware we can achieve speeds upwards of 8000 MCUPS; one of the fastest implementations of the Smith-Waterman algorithm.
Keywords
biology computing; distributed algorithms; genetics; MCUPS; Smith-Waterman algorithm; distributed algorithm; genome sequences; whole genome comparison; workstation network; Bioinformatics; Clustering algorithms; Computational biology; Databases; Genomics; Hardware; Information technology; Jacobian matrices; Sequences; Workstations;
fLanguage
English
Publisher
ieee
Conference_Titel
Parallel and Distributed Computing, 2007. ISPDC '07. Sixth International Symposium on
Conference_Location
Hagenberg
Print_ISBN
0-7695-2917
Type
conf
DOI
10.1109/ISPDC.2007.58
Filename
4271897
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