Accelerating Scalar-Product Based Sequence Alignment using Graphics Processor Units

Authors:
Cem Savas Bassoy;Svetlana Torgasin;Mei Yang;Karl-Heinz Zimmermann
Affiliations:
Institute of Computer Technology, Hamburg University of Technology, Hamburg, Germany 21071;Institute of Computer Technology, Hamburg University of Technology, Hamburg, Germany 21071;Institute of Computer Technology, Hamburg University of Technology, Hamburg, Germany 21071;Institute of Computer Technology, Hamburg University of Technology, Hamburg, Germany 21071
Venue:
Journal of Signal Processing Systems
Year:
2010

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Abstract

Alignment is one of the basic operations in molecular biology to compare sequences. The most widely used methods for multiple sequence alignment include scalar-product based alignment of groups of sequences. We show that scalar-product based alignment algorithms can be significantly speeded up by general-purpose computing on a modern commonly available graphics card. Thus the huge computational power of graphics cards can be exploited to develop high performance solutions for multiple sequence alignment.