Fine-grained GPU parallelization of pairwise local sequence alignment

• Published in: 2014 21st International Conference on High Performance Computing (HiPC) pp. 1 - 10
• Main Authors: Jain, Chirag, Kumar, Subodh
• Format: Conference Proceeding
• Language: English
• Published: IEEE 01.12.2014
• Subjects: Algorithm design and analysis; Graphics processing units; Instruction sets; Kernel; Strips; Synchronization

The Smith-Waterman algorithm is used in Bio-informatics to perform pairwise local alignment between a query sequence and a subject sequence. We present a GPU based parallel version of this algorithm that is able to perform pair-wise alignment faster than previous algorithms. In particular, it parall...