DNAfull (also known as EDNAFULL and NUC4.4) is a commonly used scoring matrix in alignment problems considering DNA and RNA strings. It uses IUPAC notation and assigns different scores to matched/mismatched nucleotides depending on the particular symbols aligned; these scores are computed based on the relative frequency of one nucleotides to be substituted for another in a collection of known alignments.
The scoring matrix is "symmetric", meaning that the score assigned to
substituting symbol
A T G C S W R Y K M B V H D N A 5 -4 -4 -4 -4 1 1 -4 -4 1 -4 -1 -1 -1 -2 T -4 5 -4 -4 -4 1 -4 1 1 -4 -1 -4 -1 -1 -2 G -4 -4 5 -4 1 -4 1 -4 1 -4 -1 -1 -4 -1 -2 C -4 -4 -4 5 1 -4 -4 1 -4 1 -1 -1 -1 -4 -2 S -4 -4 1 1 -1 -4 -2 -2 -2 -2 -1 -1 -3 -3 -1 W 1 1 -4 -4 -4 -1 -2 -2 -2 -2 -3 -3 -1 -1 -1 R 1 -4 1 -4 -2 -2 -1 -4 -2 -2 -3 -1 -3 -1 -1 Y -4 1 -4 1 -2 -2 -4 -1 -2 -2 -1 -3 -1 -3 -1 K -4 1 1 -4 -2 -2 -2 -2 -1 -4 -1 -3 -3 -1 -1 M 1 -4 -4 1 -2 -2 -2 -2 -4 -1 -3 -1 -1 -3 -1 B -4 -1 -1 -1 -1 -3 -3 -1 -1 -3 -1 -2 -2 -2 -1 V -1 -4 -1 -1 -1 -3 -1 -3 -3 -1 -2 -1 -2 -2 -1 H -1 -1 -4 -1 -3 -1 -3 -1 -3 -1 -2 -2 -1 -2 -1 D -1 -1 -1 -4 -3 -1 -1 -3 -1 -3 -2 -2 -2 -1 -1 N -2 -2 -2 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1