From: Optimizing amino acid substitution matrices with a local alignment kernel
⟨C⟩ | ||||||||
---|---|---|---|---|---|---|---|---|
Score matrix | COG distant | COG close | PFAM distant | PFAM close | ||||
SW | LA | SW | LA | SW | LA | SW | LA | |
BLOSUM62 | 0.35 | 0.42 | 0.72 | 0.73 | 0.45 | 0.49 | 0.76 | 0.78 |
BLOSUM62SWOPT | 0.42 | 0.42 | 0.70 | 0.71 | 0.49 | 0.51 | 0.75 | 0.77 |
BLOSUM62LAOPT | 0.43 | 0.51 | 0.67 | 0.69 | 0.47 | 0.54 | 0.72 | 0.75 |
PAM250 | 0.36 | 0.35 | 0.53 | 0.52 | 0.43 | 0.43 | 0.62 | 0.61 |
PAM250SWOPT | 0.38 | 0.37 | 0.57 | 0.56 | 0.44 | 0.44 | 0.65 | 0.64 |
PAM250LAOPT | 0.26 | 0.36 | 0.53 | 0.46 | 0.43 | 0.38 | 0.62 | 0.56 |
GCB | 0.13 | 0.12 | 0.33 | 0.32 | 0.12 | 0.11 | 0.37 | 0.36 |
GCBSWOPT | 0.25 | 0.24 | 0.50 | 0.50 | 0.17 | 0.19 | 0.55 | 0.56 |
GCBLAOPT | 0.14 | 0.15 | 0.39 | 0.31 | 0.16 | 0.093 | 0.44 | 0.38 |
JTT | 0.34 | 0.34 | 0.53 | 0.51 | 0.47 | 0.46 | 0.61 | 0.60 |
JTTSWOPT | 0.31 | 0.32 | 0.54 | 0.53 | 0.48 | 0.47 | 0.62 | 0.61 |
JTTLAOPT | 0.34 | 0.31 | 0.53 | 0.45 | 0.48 | 0.38 | 0.61 | 0.55 |