Title :
GPU-accelerated protein sequence alignment
Author :
Hasan, Laiq ; Kentie, Marijn ; Al-Ars, Zaid
Author_Institution :
Comput. Eng. Lab., Tech. Univ. Delft, Delft, Netherlands
fDate :
Aug. 30 2011-Sept. 3 2011
Abstract :
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.
Keywords :
bioinformatics; biological techniques; coprocessors; molecular biophysics; molecular configurations; parallel processing; proteins; GPU accelerated protein sequence alignment; Smith-Waterman algorithm; genetic databases; graphics processing units; optimal sequence alignment method; Acceleration; Bandwidth; Databases; Graphics processing unit; Instruction sets; Matrices; Proteins; Bioinformatics; Database Organization; GPUs; Protein Sequence Alignment; Smith-Waterman Algorithm; Algorithms; Databases, Protein; Proteins; Sequence Homology, Amino Acid;
Conference_Titel :
Engineering in Medicine and Biology Society, EMBC, 2011 Annual International Conference of the IEEE
Conference_Location :
Boston, MA
Print_ISBN :
978-1-4244-4121-1
Electronic_ISBN :
1557-170X
DOI :
10.1109/IEMBS.2011.6090679
