GPU-accelerated protein sequence alignment

Laiq Hasan; Marijn Kentie; Zaid Al-Ars

doi:10.1109/IEMBS.2011.6090679

GPU-accelerated protein sequence alignment

Annu Int Conf IEEE Eng Med Biol Soc. 2011:2011:2442-6. doi: 10.1109/IEMBS.2011.6090679.

Authors

Laiq Hasan¹, Marijn Kentie, Zaid Al-Ars

Affiliation

¹ Computer Engineering Lab, TU Delft, The Netherlands. L.HASAN@TUDELFT.NL

PMID: 22254835
DOI: 10.1109/IEMBS.2011.6090679

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 (CPUs) 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.

MeSH terms

Algorithms
Databases, Protein*
Proteins / chemistry*
Sequence Homology, Amino Acid*

Substances

Proteins