TY - GEN
T1 - Parallel protein sequence matching on multicore computers
AU - Sibai, Fadi N.
AU - Zaki, Nazar
PY - 2010
Y1 - 2010
N2 - STRIKE was introduced and implemented to predict protein-protein interactions where proteins interact if they contain similar substrings of amino acids. On the yeast protein interaction literature, STRIKE was shown to improve upon the existing state-of-the-art methods for protein-protein interaction prediction. Herein, we describe the parallelization of STRIKE and its multithreaded implementation and performance enhancement on multicore systems. On large protein sequence sets, the execution time of a 16-thread implementation of this bioinformatics algorithm was reduced from about a week on a unithreaded implementation on a serial uniprocessor machine to 1.5 days on one quad core x86 machine, down to 4.5 hours on 8 such quad core machines. Key optimizations to the implementation are also discussed.
AB - STRIKE was introduced and implemented to predict protein-protein interactions where proteins interact if they contain similar substrings of amino acids. On the yeast protein interaction literature, STRIKE was shown to improve upon the existing state-of-the-art methods for protein-protein interaction prediction. Herein, we describe the parallelization of STRIKE and its multithreaded implementation and performance enhancement on multicore systems. On large protein sequence sets, the execution time of a 16-thread implementation of this bioinformatics algorithm was reduced from about a week on a unithreaded implementation on a serial uniprocessor machine to 1.5 days on one quad core x86 machine, down to 4.5 hours on 8 such quad core machines. Key optimizations to the implementation are also discussed.
KW - Multithreaded computing
KW - Performance analysis
KW - Protein-protein sequence matching
KW - SIMD computing
UR - http://www.scopus.com/inward/record.url?scp=79951498968&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=79951498968&partnerID=8YFLogxK
U2 - 10.1109/SOCPAR.2010.5686630
DO - 10.1109/SOCPAR.2010.5686630
M3 - Conference contribution
AN - SCOPUS:79951498968
SN - 9781424478958
T3 - Proceedings of the 2010 International Conference of Soft Computing and Pattern Recognition, SoCPaR 2010
SP - 285
EP - 290
BT - Proceedings of the 2010 International Conference of Soft Computing and Pattern Recognition, SoCPaR 2010
T2 - 2010 International Conference of Soft Computing and Pattern Recognition, SoCPaR 2010
Y2 - 7 December 2010 through 10 December 2010
ER -