Performance with different scoring systems. The speed in billion cell updates per second (GCUPS) (logarithmic scale) is shown for 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 different scoring systems. All combinations of scoring matrices and gap penalties accepted by BLAST were tested. The matrix name is indicated above each graph, while the open and extension gap penalties are indicated on the x-axis. The query sequence was P07327 and 24 threads were running. SWPS3 would not run successfully in all cases.