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Table 2 The matrix test sets assessed in the homology search performance evaluation

From: PFASUM: a substitution matrix from Pfam structural alignments

Test set Algorithm Matrix numbers
PFASUM Search Matrices PFASUM [11,100]
Standard Search Matrices BLOSUM 50,62,80
  MD 10,20,40
  Optima 5
  PAM 120,250
  VTML 10,20,40,80,120,160,200