Table 2.
Performance evaluation
| Accession number | Query Sequence Length | CBESW (seconds) | CBESW (MCUPS) |
| O29181 | 63 | 18.45 | 445 |
| P03630 | 127 | 19.05 | 869 |
| P02232 | 143 | 19.17 | 973 |
| P05013 | 189 | 19.6 | 1,258 |
| P14942 | 222 | 20.12 | 1,439 |
| P00762 | 246 | 20.24 | 1,586 |
| P53765 | 255 | 20.43 | 1,628 |
| Q8ZGB4 | 361 | 22.04 | 2,137 |
| P10318 | 362 | 22.06 | 2,141 |
| P07327 | 374 | 22.39 | 2,179 |
| P01008 | 464 | 23.18 | 2,612 |
| P10635 | 497 | 23.69 | 2,737 |
| P58229 | 511 | 24.43 | 2,729 |
| P25705 | 553 | 24.74 | 2,916 |
| P42357 | 657 | 26.64 | 3,218 |
| P21177 | 729 | 28.06 | 3,390 |
| Q38941 | 850 | 30.45 | 3,642 |
| O60341 | 852 | 30.49 | 3,646 |
Performance evaluation of our implementation, in terms of computational time and MCUPS. All queries were run against Swiss-Prot release 55.2 comprising 130,497,792 amino acids in 362,782 sequence entries. Eighteen query sequences of length 63 to 852 amino acids were used. The gap-open penalty used is 10 and the gap-extension penalty used was 2. The BLOSUM45 scoring matrix was used.