  Sequence alignment is one of the oldest and the most famous problems in
bioinformatics. Even after 45 years, for one reason or another, this problem is
still actual; current solutions are trade-offs between execution time, memory
consumption and accuracy. We purpose SW#, a new CUDA GPU enabled and memory
efficient implementation of dynamic programming algorithms for local alignment.
In this implementation indels are treated using the affine gap model. Although
there are other GPU implementations of the Smith-Waterman algorithm, SW# is the
only publicly available implementation that can produce sequence alignments on
genome-wide scale. For long sequences, our implementation is at least a few
hundred times faster than a CPU version of the same algorithm.
