DOPA: GPU-based protein alignment using database and memory access optimizations

BMC Research Notes

Table 1 Performance results with Swiss-Prot

Query sequence	Length	Execution time (seconds)	Performance (GCUPS)
P02232	144	1.24	21.35
P05013	189	1.65	21.06
P14942	222	1.93	21.15
P07327	375	3.24	21.28
P01008	464	3.99	21.38
P03435	567	4.89	21.32
P27895	1000	8.60	21.38
P07756	1500	12.91	21.36
P04775	2005	17.27	21.35
P19096	2504	21.54	21.37
P28167	3005	25.88	21.35
P0C6B8	3564	30.67	21.37
P20930	4061	34.97	21.35
Q9UKN1	5478	47.15	21.36

The table displays performance results, where execution time in seconds and performance in GCUPS are given for query sequences of varying lengths taken from Swiss-Prot and aligned against the sequences in the same database.

ISSN: 1756-0500