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Parallel Implementation of DNA Sequences Matching Algorithms using PWM on GPU Architecture (ACM)

Publication Year: 
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.

Paper available at ACM.

Institution: 
Department of Computer Science and Engineering, College of Engineering Roorkee, India.
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