TABLE 1.
Scoring matrix target identity, information content, and alignment length.
| Matrix | gap1 penalty |
% ident. |
bits / pos. |
random aln. len. |
50-bit length |
|---|---|---|---|---|---|
| SSEARCH version 36.3.6 | |||||
|
| |||||
| BLOSUM502 | 10/2 | 25.3 | 0.21 | 160 | 238 |
| BLOSUM62 | 11/1 | 28.9 | 0.40 | 86 | 125 |
| VTML 1602,3 | 12/2 | 23.9 | 0.25 | 139 | 200 |
| VTML 140 | 10/1 | 28.4 | 0.44 | 82 | 114 |
| VTML 120 | 11/1 | 32.1 | 0.54 | 62 | 93 |
| VTML 80 | 10/1 | 40.5 | 0.74 | 47 | 68 |
| VTML 40 | 13/1 | 64.7 | 1.92 | 18 | 26 |
| VTML 20 | 15/2 | 86.1 | 3.30 | 11 | 15 |
| VTML 10 | 16/2 | 90.9 | 3.87 | 9 | 13 |
|
| |||||
| BLAST version 2.2.27+ | |||||
|
| |||||
| BLOSUM502 | 13/2 | 29.4 | 0.39 | 85 | 128 |
| BLOSUM62 | 11/1 | 29.6 | 0.41 | 82 | 122 |
| BLOSUM80 | 10/1 | 32.0 | 0.48 | 69 | 104 |
| PAM70 | 10/1 | 33.9 | 0.58 | 56 | 86 |
| PAM30 | 9/1 | 45.9 | 0.90 | 34 | 56 |
1
Gap open/extend penalty, where the total penalty is open+r*extend, where r is the number of residues in the gap. Thus, a 10/2 penalty produces a penalty of 12 for a one residue gap, 14 for two residues, etc.
2
Scaled in 1/3-bit units; all other matrices are scaled in 1/2-bit units.
3
As calculated according to Mueller et al. (2002).
Median percent identity, bits per aligned position, alignment length, and alignment length required for a 50-bit score based on searches of 140 random sequences against 240,000 real protein sequences using the specified scoring matrix and gap penalties.