Accelerating Scalar-Product Based Sequence Alignment using Graphics Processor Units
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.
alignment performance progressive alignment graphics processor card basic linear algebra subprograms