Skip to main content

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.