title: GPU-accelerated protein sequence alignment.
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.
authors.affiliation: Computer Engineering Lab, TU Delft, The Netherlands. L.HASAN@TUDELFT.NL
authors.forename: Laiq
authors.initials: L
authors.lastname: Hasan
authors.forename: Marijn
authors.initials: M
authors.lastname: Kentie
authors.forename: Zaid
authors.initials: Z
authors.lastname: Al-Ars
mesh_terms: D000465:Algorithms; D030562:Databases, Protein; D011506:Proteins / Q000737:chemistry*; D017386:Sequence Homology, Amino Acid
chemical_list: D011506:Proteins