Title :
A GPU based implementation of Needleman-Wunsch algorithm using skewing transformation
Author :
Anuj Chaudhary;Deepkumar Kagathara;Vibha Patel
Author_Institution :
Department of CSE, Institute of Technology, Nirma University, Ahmedabad, India 382481
Abstract :
We present a new parallel approach of Needleman-Wunsch algorithm for global sequence alignment. This approach uses skewing transformation for traversal and calculation of the dynamic programming matrix. We compare the execution time of sequential CPU based implementation with two parallel GPU based implementations: Single-kernel invocation with lock-free block synchronization and multi-kernel invocation at block-synchronization points. Both the GPU based implementations gave upto 6 times performance improvement over the sequential CPU based implementation.
Keywords :
"Graphics processing units","Synchronization","Heuristic algorithms","Dynamic programming","Kernel","Proteins","Central Processing Unit"
Conference_Titel :
Contemporary Computing (IC3), 2015 Eighth International Conference on
Print_ISBN :
978-1-4673-7947-2
DOI :
10.1109/IC3.2015.7346733
