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Table 3 MI-based error of subfamily-identifying methods.

From: An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies

A. Generated data and LacI
  SDPsite bete Giant component Protein keys FASS S-method SDPclust  
Generated family 1 0.58 0.00 1.00 0.00 0.00 0.00 0.00  
Generated family 2 0.94 1.00 1.00 0.94 0.95 0.94 0.00  
LacI 0.11 0.12 0.20 0.16 0.93 1.00 0.10  
B. Enzyme dataset
  SDPsite Giant component Protein keys FASS S-method SDPclust # EC # sequences
PF00108 0.000 0.633 0.621 0.687 0.786 0.679 2 22
PF00128 0.801 0.552 0.586 N/A N/A 0.544 10 154
PF00135 0.429 0.583 0.548 N/A N/A 0.486 4 129
PF00215 0.759 0.878 0.803 N/A 0.758 0.751 3 92
PF00278 0.321 0.608 0.538 0.311 0.577 0.277 3 55
PF00293 0.239 0.449 0.200 N/A N/A 0.237 6 205
PF00348 1.000 0.352 0.555 0.674 0.764 0.372 3 16
PF00351 0.292 1.000 0.495 N/A N/A 0.573 3 6
PF00579 0.492 0.749 0.603 0.629 0.764 0.472 2 41
PF00583 0.132 0.326 0.261 N/A N/A 0.311 10 244
PF00590 1.000 0.383 0.141 0.603 0.561 0.070 7 22
PF00755 0.544 0.407 0.522 N/A N/A 0.431 4 22
PF00871 1.000 0.675 0.709 N/A N/A 0.752 3 12
PF00896 0.000 0.594 0.000 N/A N/A 0.000 2 13
PF00962 0.000 0.654 0.399 0.285 0.367 0.494 2 17
PF01048 0.000 0.722 0.571 0.912 0.912 0.912 2 16
PF01112 0.000 0.500 0.333 N/A N/A 0.333 2 7
PF01467 0.756 0.515 0.432 0.543 0.295 0.142 6 67
PF01712 0.500 0.387 0.521 N/A N/A 0.500 4 14
PF02274 0.000 0.788 0.707 0.000 1.000 0.707 2 32
PF03171 0.668 0.096 0.196 0.812 0.813 0.075 11 153
Overall distance*0.184 0.276 0.204 0.250 0.172 0.165    
  1. The following Web-servers were used for testing: SDPsite http://bioinf.fbb.msu.ru/SDPsite/index.jsp, bete http://phylogenomics.berkeley.edu/cgi-bin/SCI-PHY/input_SCI-PHY.py, giant component (unavialable, implemented in house), Protein Keys http://www.proteinkeys.org/proteinkeys/, FASS, S-method http://treedet.bioinfo.cnio.es/, SDPclust http://bioinf.fbb.msu.ru/SDPfoxWeb/main.jsp. The best performing method is marked in bold.
  2. * all groups are treated together, as members of the same family.