Performance dependency on number of threads and query length. The speed in billion cell updates per second (GCUPS) of the BLAST (red), BLAST+ (orange), SWIPE (black), and SWPS3 (green) programs, as well as STRIPED compiled with the GNU (light blue) and Intel (dark blue) compiler, using a variable number of threads and queries of varying length. (A) Number of threads ranging from 1 to 24 and the 375 residue long P07327 query sequence. (B) Query sequences ranging from 24 to 5478 residues in length and 24 threads. (C) Query sequences of varying length and 1 thread. All scales are logarithmic. The BLOSUM62 matrix and gap open and extension penalties of 11 and 1, respectively, were used in all cases.
Rognes BMC Bioinformatics 2011 12:221 doi:10.1186/1471-2105-12-221