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 have shown that scalar-product based alignment algorithms can be significantly speeded up by general-purpose computing on a modern commonly available graphics card. This allows to develop high performance solutions for multiple-sequence alignment by utilizing the huge computational power of graphics cards.
Key Words alignment - progressive alignment - graphics processor card - basic linear algebra subprograms - performance
Literature
- C.S. Bassoy, M. Yang, S. Torgasin, K.-H. Zimmermann: Accelerating scalar-product based sequence alignment using graphics processor units. J. Sig. Proc. Syst., 1939-8115 (online), 2009.
- GPGPU.org
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