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Return NUC44 scoring matrix for nucleotide sequences


ScoringMatrix = nuc44
[ScoringMatrix, MatrixInfo] = nuc44


ScoringMatrix = nuc44 returns the scoring matrix. The nuc44 scoring matrix uses ambiguous nucleotide codes and probabilities rounded to the nearest integer.

Scale = 0.277316

Expected score = -1.7495024, Entropy = 0.5164710 bits

Lowest score = -4, Highest score = 5

Order: A C G T R Y K M S W B D H V N

[ScoringMatrix, MatrixInfo] = nuc44 returns a structure with information about the matrix with fields Name and Order.


The NUC44 scoring matrix is supplied by NCBI and is used by the BLAST suite of programs. For more information, see

Version History

Introduced before R2006a