Parallel implementation of DNA sequences matching algorithms using PWM on GPU architecture Online publication date: Sat, 24-Jan-2015
by Rahul Sharma, Nitin Gupta, Vipin Narang, Ankush Mittal
International Journal of Bioinformatics Research and Applications (IJBRA), Vol. 7, No. 2, 2011
Abstract: Positional Weight Matrices (PWMs) are widely used in representation and detection of Transcription Factor Of Binding Sites (TFBSs) on DNA. We implement online PWM search algorithm over parallel architecture. A large PWM data can be processed on Graphic Processing Unit (GPU) systems in parallel which can help in matching sequences at a faster rate. Our method employs extensive usage of highly multithreaded architecture and shared memory of multi-cored GPU. An efficient use of shared memory is required to optimise parallel reduction in CUDA. Our optimised method has a speedup of 230-280x over linear implementation on GPU named GeForce GTX 280.
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