Title: Parallel implementation of DNA sequences matching algorithms using PWM on GPU architecture

Authors: Rahul Sharma, Nitin Gupta, Vipin Narang, Ankush Mittal

Addresses: Department of Computer Science and Engineering, College of Engineering Roorkee, India. ' Department of Computer Science and Engineering, College of Engineering Roorkee, India. ' Gnomic Institute of Singapore, Singapore. ' Department of Computer Science and Engineering, College of Engineering Roorkee, India

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.

Keywords: GPU; graphic processing unit; PWM; positional weight matrices; TFBSs; transcription factor; binding sites; multithread hierarchy; parallel implementation; shared memory; DNA sequences; sequence matching.

DOI: 10.1504/IJBRA.2011.040097

International Journal of Bioinformatics Research and Applications, 2011 Vol.7 No.2, pp.202 - 215

Received: 24 Aug 2010
Accepted: 13 Dec 2010

Published online: 13 May 2011 *

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