# Glossary

## DNAfull

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 $x$ for symbol $y$ is the same as that of substituting $y$ for $x$. The matrix itself can be found below.

    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