Alignment is the fundamental operation in molecular biology for comparing biomolecular sequences. The most widely used method for aligning groups of alignments is based on the alignment of the profiles corresponding to the groups. We show that profile-profile alignment can be significantly speeded up by general purpose computing on a modern commodity graphics card. In this way, the huge computational power of graphics cards can be exploited to develop high performance solutions for multiple sequence alignment.
Keywords Alignment · Progressive alignment · Graphics processor card · Basic linear algebra subprograms · Performance.
M.K. Hanif, K.-H. Zimmermann: Accelerating Profile-Profile Alignment Using Graphics Processor Units. J. Sig. Proc. Systems, submitted.
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