Fig. 3

Progression of the maximum achieved coverage of CorBLOSUM-, RBLOSUM- and BLOSUM-type matrices for all ASTRAL40 test databases. The upper row shows the results for the respective BLOSUM50 entropy level, the lower row for BLOSUM62 entropy level. Insignificant coverage differences between CorBLOSUM and BLOSUM are indicated by an O and between CorBLOSUM and RBLOSUM by a small an X above the bars. The corresponding gap parameter settings are listed in Additional file 2. Notably, the coverage increases for all tested substitution matrices dramatically with the introduction of the semi-automatic database generation of SCOPe. For the BLOSUM50 entropy level, CorBLOSUM-type matrices performed at least as good as their BLOSUM counterparts in ∼84 % of all tested scenarios and in ∼49 % showed a similar or better performance than the RBLOSUM-type matrices. For the BLOSUM62 entropy level CorBLOSUM matrices showed equally as good or better performance than BLOSUM in ∼67 % while improving performance over RBLOSUM in ∼60 % of all analyzed ASTRAL40 scenarios