Figure 4
From: Optimizing amino acid substitution matrices with a local alignment kernel
Coverage vs Error Per Query plots for the COG distant (identity less than 20%) test set. In the graph, BLOSUM62SWOPT and BLOSUM62LAOPT mean the amino acid substitution matrices optimized starting from BLOSUM62 with the SW algorithm and the LA kernel, respectively. SW scores and LA scores mean the E-values of the SW algorithm and the LA kernel algorithm, respectively. All of the proteins in the COG test set were compared with each other using the SW algorithm or the LA kernel with BLOSUM62LAOPT or BLOSUM62SWOPT. Curves located further to the right side indicate better performance.