Table 2.
Over-alignment parameters for some common scoring schemes
| Matrix | GOP | GEP | λ | c | E(length) | P(length = 0) | Comments |
|---|---|---|---|---|---|---|---|
| BLOSUM45 | 15 | 2 | 0.203 | 0.674 | 6.72 | 0.490 | |
| BLOSUM50 | 10 | 2 | 0.141 | 0.714 | 22.89 | 0.369 | FASTA 3.5 default |
| BLOSUM62 | 7 | 2 | 0.239 | 0.700 | 7.80 | 0.483 | WU BLAST 2.0 default |
| BLOSUM62 | 11 | 1 | 0.267 | 0.669 | 5.53 | 0.532 | NCBI BLAST 2.2.17 default |
| BLOSUM62 | 11 | 2 | 0.299 | 0.645 | 2.96 | 0.589 | |
| BLOSUM62 | 10 | 4 | 0.309 | 0.633 | 2.37 | 0.605 | Matcher default |
| BLOSUM62 | 9.5 | 0.5 | – | – | – | – | Water, Supermatcher default |
| BLOSUM80 | 10 | 1 | 0.300 | 0.609 | 2.81 | 0.611 | |
| HoxD55 | 400 | 30 | 0.00592 | 0.802 | 23.50 | 0.330 | UCSC genome alignments |
| HoxD70 | 400 | 30 | 0.00908 | 0.694 | 4.53 | 0.486 | BLASTZ v7 default |
| +1/−1 | 2 | 1 | 0.916 | 0.997 | 2.30 | 0.602 | |
| +1/−3 | 5 | 2 | 1.332 | 1.000 | 0.36 | 0.736 | NCBI BLAST 2.2.17 default |
| +2/−3 | 5 | 2 | 0.593 | 0.790 | 0.87 | 0.666 | NCBI BLAST website default |
| +5/−4 | 12 | 4 | 0.133 | 0.789 | 10.80 | 0.351 | FASTA 3.5, Matcher default |
| +5/−4 | 0 | 10 | 0.0765 | 0.9294 | 40.51 | 0.226 | WU BLAST 2.0 default |
| +5/−4 | 9.5 | 0.5 | – | – | – | – | Water, Supermatcher default |
Protein parameters are for Robinson-Robinson frequencies. DNA parameters are for 60% AT.
*Dashes represent that simulations were unable to determine whether the scoring scheme was in the local regime.