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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