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Table 4 Best performing substitution matrices of the PFASUM Search Matrices and Standard Search Matrices sets for the three test scenarios

From: PFASUM: a substitution matrix from Pfam structural alignments

Database Matrix Gap parameters Coverage
ASTRAL20 VTML200 -14/-1 0.1598
  PFASUM60 -16/-1 0.1706
ASTRAL40 VTML200 -14/-1 0.4392
  PFASUM43 -13/-1 0.4448
ASTRAL70 VTML200 -9/-2 0.5459
  PFASUM31 -13/-2 0.5508