DocumentCode :
2160532
Title :
Modeling tryptic digestion on the Cell BE processor
Author :
Green, James R. ; Mahmoud, Hanan ; Dumontier, Michel
Author_Institution :
Dept. of Syst. & Comput. Eng., Carleton Univ., Ottawa, ON
fYear :
2009
fDate :
3-6 May 2009
Firstpage :
701
Lastpage :
705
Abstract :
The cell BE is a heterogeneous multi-core processor offering multiple levels of parallelism. When these are properly leveraged, the cell BE demonstrates impressive performance acceleration for several high performance computing applications, including exact string matching on streaming data. The present study investigates the suitability of the cell BE for a string matching problem of relevance to proteomics - the identification of tryptic digest points based on the presence of a short sequence motif. Three string matching algorithms are implemented and evaluated over several proteomic datasets. In its first application to bioinformatics, Parabix, a method of high-throughput XML stream processing which relies on bit transposition and the effective use of single-instruction multiple-data (SIMD) instructions, is applied here with great success. This method performs very well when the protein database is pre-processed in the form of parallel bit streams. Double buffering is also critical to hide the latency of DMA data transfers. Performance results are computed for both the cycle-accurate cell BE simulator and also using real hardware. This problem is also placed in the larger context of using the cell BE to achieve hypothesis-driven protein identification.
Keywords :
XML; bioinformatics; file organisation; microprocessor chips; parallel processing; string matching; cell BE processor; data streaming; double buffering; heterogeneous multicore processor; high-throughput XML stream processing; hypothesis-driven protein identification; memory memory access; parallel bit streams; parallel processing; protein database; proteomic datasets; single-instruction multiple-data instruction; string matching; tryptic digestion modeling; Acceleration; Bioinformatics; Databases; Delay; High performance computing; Multicore processing; Parallel processing; Proteins; Proteomics; XML; parallel processing; string matching;
fLanguage :
English
Publisher :
ieee
Conference_Titel :
Electrical and Computer Engineering, 2009. CCECE '09. Canadian Conference on
Conference_Location :
St. John´s, NL
ISSN :
0840-7789
Print_ISBN :
978-1-4244-3509-8
Electronic_ISBN :
0840-7789
Type :
conf
DOI :
10.1109/CCECE.2009.5090220
Filename :
5090220
Link To Document :
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