Table 3.
fasta36 built-in scoring matrices
| name | abbrev | gap-penalties | bit-scale | notes |
|---|---|---|---|---|
| BLOSUM series (Henikoff and Henikoff, 1992) | ||||
|
| ||||
| BLOSUM 50 | BL50 | -10/-2 | bits/3 | |
| BLOSUM 62 | BP62 | -11/-1 | bits/2 | same as BLASTP |
| BLOSUM 62 | BL62 | -7/-1 | bits/2 | |
| BLOSUM 80 | BL80 | -10/-2 | bits/2 | |
|
| ||||
| Dayhoff PAM series (Schwartz and Dayhoff, 1978) | ||||
|
| ||||
| PAM 250 | P250 | -10/-2 | bits/3 | |
| PAM 120 | P120 | -14/-3 | bits/3 | |
|
| ||||
| Modern PAM (MDM) series (Jones et al., 1992) | ||||
|
| ||||
| MDM 10 | MD10 | -23/-4 | bits/3 | |
| MDM 20 | MD20 | -22/-4 | bits/3 | |
| MDM 40 | MD40 | -21/-4 | bits/3 | |
|
| ||||
| VTML series (Mueller et al., 2002) | ||||
|
| ||||
| VTML 10 | VT10 | -16/-2 | bits/2 | |
| VTML 20 | VT20 | -15/-2 | bits/2 | |
| VTML 40 | VT40 | -15/-2 | bits/2 | |
| VTML 80 | VT80 | -15/-2 | bits/2 | |
| VTML 120 | VT120 | -15/-2 | bits/2 | |
| VTML 160 | VT160 | -15/-2 | bits/2 | |
| VTML 200 | VT200 | -15/-2 | bits/2 | |
|
| ||||
| Optima5 | OPT5 | -18/-2 | bits/5 | (Kann and Goldstein, 2002) |