title: Parallel implementation of DNA sequences matching algorithms using PWM on GPU architecture.
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.
authors.affiliation: Department of Computer Science and Engineering, College of Engineering Roorkee, India. rahulsrma26@gmail.com
authors.forename: Rahul
authors.initials: R
authors.lastname: Sharma
authors.forename: Nitin
authors.initials: N
authors.lastname: Gupta
authors.forename: Vipin
authors.initials: V
authors.lastname: Narang
authors.forename: Ankush
authors.initials: A
authors.lastname: Mittal
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D004247:DNA / Q000737:chemistry*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA