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Table 1 This table summarizes the outcome of 100 resampling or bootstrapping tests done using the two data sets (prokaryotic lyases and SH2 containing proteins) with different parameter combinations. For each simulation the average adjusted rand index [44] has been calculated. The row marked in italic bold corresponds to the parameters used in the reference protocol. The values marked in bold indicate the changes made compared to the reference protocol.

From: JACOP: A simple and robust method for the automated classification of protein sequences with modular architecture

     Prokaryotic lyases SH2 containing proteins
Probe length Pruning threshold Coverage Scoring system Resampling Bootstrap Resampling Bootstrap
25 160 3 Blosum62/-12/-1 0.959 0.991 0.844 0.854
50 160 3 Blosum62/-12/-1 1 1 0.932 0.937
100 160 3 Blosum62/-12/-1 0.969 0.887 0.689 0.735
50 40 3 Blosum62/-12/-1 0.971 0.810 0.777 0.732
50 80 3 Blosum62/-12/-1 1 0.982 0.753 0.803
50 120 3 Blosum62/-12/-1 1 1 0.895 0.897
50 160 3 Blosum62/-12/-1 1 1 0.932 0.937
50 200 3 Blosum62/-12/-1 1 1 0.948 0.935
50 160 1 Blosum62/-12/-1 1 0.991 0.919 0.812
50 160 2 Blosum62/-12/-1 1 0.996 0.878 0.937
50 160 3 Blosum62/-12/-1 1 1 0.932 0.937
50 160 3 Blosum45/-13/-3 1 0.985 0.939 0.839
50 160 3 Blosum62/-12/-1 1 1 0.932 0.937
50 160 3 Blosum80/-10/-1 0.999 0.991 0.909 0.859