GPU-accelerated protein sequence alignment

descriptionPublicationkeyboard_double_arrow_right Article , Conference object 01 Aug 2011Publisher:IEEEJournal:2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society

Authors: Laiq Hasan; Marijn Kentie; Zaid Al-Ars;

doi: 10.1109/iembs.2011.6090679

pmid: 22254835

GPU-accelerated protein sequence alignment

- Summary
- Subjects
- Metrics

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.

Related Organizations

Delft University of Technology
Netherlands

Keywords

Sequence Homology, Amino Acid, Proteins, Databases, Protein, Algorithms

Impact byBIP!

	selected citations These citations are derived from selected sources. This is an alternative to the "Influence" indicator, which also reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).	3
	popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.	Average
	influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).	Average
	impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.	Average