Table 1.

SW# and CUDAlign run time comparison for different NVIDIA GPU cards and sequence lengths

Sequences size	CPU	GTX 560 CUDAligna	GTX 570 SW#	GTX 690b SW#
2 × 172 Kb	660 s	2.1 s	1.5 s	2.6 s
0.5 × 0.5 Mb	9090 s	11.8 s	9.4 s	5.8 s
3.1 × 3.3 Mb	—	367 s	296 s	119 s
59 × 24 Mb	—	47123 s	40359 s	16263 s
33 × 47 Mb	—	30369 s	59228 s	23614 s

Note: CPU results are presented only for shorter sequences.

^aCUDAlign results are taken from the original article (Sandes and Melo, 2013).

^bDual GPU card.