Parallel implementation of DNA sequences matching algorithms using PWM on GPU architecture. (16th May 2011)

• Record Type: Journal Article
• Authors: Sharma, Rahul; Gupta, Nitin; Narang, Vipin; Mittal, Ankush
• Is Part Of: International journal of bioinformatics research and applications. Volume 7:Number 2(2011)
• Page Start: 202
• Page End: 215
• Publication Date: 2011-05-16
• Subjects: GPU -- graphic processing unit -- PWM -- positional weight matrices -- TFBSs -- transcription factor of binding sites -- thread hierarchy -- parallel implementation -- shared memory; Bioinformatics -- Periodicals; 570.285
• Languages: English
• ISSNs: 1744-5485

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.