GPU-accelerated protein sequence alignment

Author

Hasan, Laiq ; Kentie, Marijn ; Al-Ars, Zaid

Author_Institution

Comput. Eng. Lab., Tech. Univ. Delft, Delft, Netherlands

fYear

2011

fDate

Aug. 30 2011-Sept. 3 2011

Firstpage

2442

Lastpage

2446

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;

fLanguage

English

Publisher

ieee

Conference_Titel

Engineering in Medicine and Biology Society, EMBC, 2011 Annual International Conference of the IEEE

Conference_Location

Boston, MA

ISSN

1557-170X

Print_ISBN

978-1-4244-4121-1

Electronic_ISBN

1557-170X

Type

conf

DOI

10.1109/IEMBS.2011.6090679

Filename

6090679