Table 2.
Accuracy and Confidence values of global alignment
| 30 PAM | 60 PAM | |||||||
|---|---|---|---|---|---|---|---|---|
| Matrix | Gap open | Gap extention | Accuracy | Confi-dence | Gap open | Gap extention | Accuracy | Confi-dence |
| PAM30 | 18.0 | 2.0 | 0.9910 | 0.9907 | 25.0 | 2.0 | 0.9604 | 0.9600 |
| PAM60 | 17.0 | 1.0 | 0.9916 | 0.9911 | 21.0 | 1.0 | 0.9610 | 0.9607 |
| PAM120 | 13.0 | 1.0 | 0.9914 | 0.9908 | 13.0 | 1.0 | 0.9621 | 0.9599 |
| PAM250 | 9.0 | 1.0 | 0.9901 | 0.9894 | 13.0 | 1.0 | 0.9610 | 0.9575 |
| Blosum45 | 15.0 | 1.0 | 0.9901 | 0.9893 | 14.0 | 1.0 | 0.9559 | 0.9531 |
| Blosum50 | 14.0 | 1.0 | 0.9902 | 0.9895 | 17.0 | 1.0 | 0.9563 | 0.9533 |
| Blosum62 | 16.0 | 1.0 | 0.9906 | 0.9900 | 19.0 | 1.0 | 0.9575 | 0.9549 |
| Gonnet250 | 11.0 | 1.0 | 0.9899 | 0.9890 | 11.0 | 1.0 | 0.9551 | 0.9514 |
| Gonnet_p | 7.0 | 1.0 | 0.9879 | 0.9864 | 10.0 | 1.0 | 0.9460 | 0.9398 |
| Optima | 10.0 | 1.0 | 0.9899 | 0.9891 | 14.0 | 1.0 | 0.9557 | 0.9520 |
| VTML250 | 10.0 | 1.0 | 0.9894 | 0.9885 | 12.0 | 1.0 | 0.9555 | 0.9515 |
| MIQS | 11.0 | 1.0 | 0.9897 | 0.9888 | 15.0 | 1.0 | 0.9564 | 0.9527 |
| Pfasum050 | 14.0 | 1.0 | 0.9899 | 0.9890 | 16.0 | 1.0 | 0.9574 | 0.9542 |
| Pfasum100 | 11.0 | 1.0 | 0.9901 | 0.9892 | 14.0 | 1.0 | 0.9573 | 0.9542 |
| Crooks | 13.0 | 1.0 | 0.9900 | 0.9893 | 17.0 | 1.0 | 0.9555 | 0.9524 |
| CCF53 | 11.0 | 1.0 | 0.9900 | 0.9892 | 13.0 | 1.0 | 0.9563 | 0.9534 |
| Moll60 | 12.0 | 1.0 | 0.9900 | 0.9893 | 16.0 | 1.0 | 0.9564 | 0.9531 |
| Johnson | 18.0 | 1.0 | 0.9904 | 0.9899 | 23.0 | 1.0 | 0.9564 | 0.9547 |
| Prlic | 18.0 | 1.0 | 0.9896 | 0.9889 | 24.0 | 1.0 | 0.9532 | 0.9503 |
| Blake | 22.0 | 1.0 | 0.9880 | 0.9879 | 30.0 | 1.0 | 0.9468 | 0.9458 |
| Benner | 9.0 | 1.0 | 0.9878 | 0.9867 | 12.0 | 1.0 | 0.9452 | 0.9407 |
| Miyazawa | 21.0 | 1.0 | 0.9864 | 0.9855 | 22.0 | 1.0 | 0.9432 | 0.9408 |
| Data set | 120 PAM | Bali Base | ||||||
| Matrix | Gap open | Gap extention | Accuracy | Confi-dence | Gap open | Gap extention | Accuracy | Confi-dence |
| PAM30 | 30.0 | 4.0 | 0.8065 | 0.7991 | 24.0 | 4.0 | 0.6257 | 0.6215 |
| PAM60 | 26.0 | 3.0 | 0.8174 | 0.8080 | 20.0 | 3.0 | 0.6301 | 0.6236 |
| PAM120 | 19.0 | 1.0 | 0.8189 | 0.8152 | 16.0 | 2.0 | 0.6287 | 0.6205 |
| PAM250 | 17.0 | 1.0 | 0.8325 | 0.8241 | 11.0 | 2.0 | 0.6310 | 0.6240 |
| Blosum45 | 22.0 | 1.0 | 0.7949 | 0.7855 | 13.0 | 1.0 | 0.6495 | 0.6473 |
| Blosum50 | 21.0 | 1.0 | 0.7925 | 0.7866 | 16.0 | 2.0 | 0.6523 | 0.6433 |
| Blosum62 | 24.0 | 2.0 | 0.7972 | 0.7877 | 19.0 | 2.0 | 0.6533 | 0.6455 |
| Gonnet250 | 16.0 | 1.0 | 0.8129 | 0.8037 | 11.0 | 1.0 | 0.6592 | 0.6541 |
| Gonnet_p | 13.0 | 1.0 | 0.7870 | 0.7729 | 7.0 | 1.0 | 0.6470 | 0.6353 |
| Optima | 17.0 | 1.0 | 0.7907 | 0.7830 | 13.0 | 1.0 | 0.6515 | 0.6463 |
| VTML250 | 15.0 | 1.0 | 0.8110 | 0.8017 | 11.0 | 1.0 | 0.6544 | 0.6486 |
| MIQS | 18.0 | 1.0 | 0.8046 | 0.7964 | 13.0 | 1.0 | 0.6518 | 0.6479 |
| Pfasum050 | 21.0 | 1.0 | 0.8015 | 0.7939 | 15.0 | 2.0 | 0.6599 | 0.6507 |
| Pfasum100 | 18.0 | 1.0 | 0.7973 | 0.7891 | 12.0 | 1.0 | 0.6527 | 0.6499 |
| Crooks | 18.0 | 2.0 | 0.7921 | 0.7823 | 14.0 | 2.0 | 0.6553 | 0.6470 |
| CCF53 | 18.0 | 1.0 | 0.7923 | 0.7841 | 14.0 | 1.0 | 0.6488 | 0.6429 |
| Moll60 | 19.0 | 1.0 | 0.7819 | 0.7762 | 12.0 | 2.0 | 0.6484 | 0.6403 |
| Johnson | 29.0 | 2.0 | 0.8011 | 0.7935 | 19.0 | 3.0 | 0.6524 | 0.6456 |
| Prlic | 13.0 | 1.0 | 0.7870 | 0.7729 | 18.0 | 2.0 | 0.6476 | 0.6427 |
| Blake | 30.0 | 4.0 | 0.7608 | 0.7547 | 24.0 | 3.0 | 0.6444 | 0.6419 |
| Benner | 16.0 | 1.0 | 0.7385 | 0.7282 | 10.0 | 1.0 | 0.5917 | 0.5848 |
| Miyazawa | 30.0 | 2.0 | 0.7539 | 0.7449 | 20.0 | 3.0 | 0.6024 | 0.5936 |
The optimal values of the alignment quality (Accuracy, Confidence) with the corresponding values of the penalty function parameters (GOP, GEP) are given. Data were obtained for all matrices examined, on test sets of the generated sequences: 30 PAM, 60 PAM, 120 PAM, and on Balibase [18] sequences. A full set of alignment quality values for the entire set of tested GOP and GEP parameters is given in Additional files 1, 2: Table S1, Table S2