Main Content


Return Gonnet scoring matrix




gonnet returns the Gonnet matrix.

The Gonnet matrix is the recommended mutation matrix for initially aligning protein sequences. Matrix elements are ten times the logarithmic of the probability that the residues are aligned divided by the probability that the residues are aligned by chance, and then matrix elements are normalized to 250 PAM units.

Expected score = -0.6152, Entropy = 1.6845 bits, Lowest score = -8, Highest score = 14.2


A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *


[1] Gaston, H., Gonnet, M., Cohen, A., and Benner, S. (1992). Exhaustive matching of the entire protein sequence database. Science. 256, 1443–1445.

Version History

Introduced before R2006a