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Table 3 The pair-wise comparison of group-specific matrices vs. general-purpose matrices.

From: Protein sequence alignment with family-specific amino acid similarity matrices

  VTML GONN BL30 BL50 BL62 PAM120 PAM160 PAM250 BC-STR STRM
FSM-SUP 50;5 86;1 120;5 74;6 63;0 106;3 110;4 114;3 67;7 93;0
FSM-TWI 15;2 20;1 41;3 21;9 19;4 36;0 37;1 35;0 21;4 24;1
Adaptive FSM-SUP 35;6 70;2 103;7 50;9 45;3 90;4 96;4 98;4 60;14 73;1
  1. Matrix names are the same as in Table 1. Abbreviations: FSM-SUP - family-specific matrices tested on groups from the SUP sub-set. FSM-TWI - fold-specific matrices tested on groups from the TWI sub-set. Adaptive FSM-SUP - the adaptive family-specific matrix selection procedure tested on the groups from the SUP sub-set. The results shown are for groups with 10 or more reference alignments (244 groups in the SUP sub-set, 131 groups in the TWI sub-set). A cell formed by the intersection of row i and column j shows the results of the pair-wise comparison of matrices (i, j), and contains two numbers: first is the number of groups on which matrix i performs significantly better than j, second is the number of groups on which matrix j performs significantly better than i.