Table 4

Correlation between different substitution tables and the profile-profile scores. Three tables, BLOSUM62, GONNET and JTT, are derived from sequence alignments while SDM is a structure based table. Three tables derived from ProfNet are also included, using the all (trained on data from all SCOP levels), su (trained on superfamily related data) and S-score (trained on superfamily related data and using the S-score as a classifier instead of a binary classifier) versions. STRUCTAL is a substitution table constructed from the residue matches found in the structurally aligned superfamily-related training set. The highest correlations are shown in bold.

subst. table

prob_score

ProfNet_S

BLOSUM62

0.95

0.75

GONNET

0.93

0.75

JTT

0.87

0.70

SDM

0.89

0.73

STRUCTAL

0.85

0.82

ProfNet_su

0.83

0.96

ProfNet_all

0.83

0.95

ProfNet_S

0.80

1

Ohlson and Elofsson BMC Bioinformatics 2005 6:253   doi:10.1186/1471-2105-6-253