GPU-accelerated protein sequence alignment

• Published in: 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society Vol. 2011; pp. 2442 - 2446
• Main Authors: Hasan, L., Kentie, M., Al-Ars, Z.
• Format: Conference Proceeding Journal Article
• Language: English
• Published: United States IEEE 01-01-2011
• Subjects: Acceleration; Algorithms; Bandwidth; Bioinformatics; Database Organization; Databases, Protein; GPUs; Graphics processing unit; Instruction sets; Matrices; Protein Sequence Alignment; Proteins; Proteins - chemistry; Sequence Homology, Amino Acid; Smith-Waterman Algorithm
• ISBN: 9781424441211; 1424441218
• ISSN: 1094-687X; 1557-170X; 1558-4615
• DOI: 10.1109/IEMBS.2011.6090679

Smith-Waterman (S-W) algorithm is an optimal sequence alignment method and is widely used for genetic databases. This paper presents a Graphics Processing Units (GPUs) accelerated S-W implementation for protein sequence alignment. The paper proposes a new sequence database organization and several optimizations to reduce the number of memory accesses. The new implementation achieves a performance of 21.4 GCUPS, which is 1.13 times better than the state-of-the-art implementation on an NVIDIA GTX 275 graphics card.