substitution-matrix
NAME
substitution-matrix - format for 26 by 26-letter substitu-
tion matrix.
DESCRIPTION
The substitution matrix is a lower-diagonal matrix consist-
ing of 26 rows and columns. Unused entries are typically
filled with zeroes. Other entries contain a score to be
applied when a match is found. For example, if A is matched
with A, the score in the first row and column is added to
the cumulative score. If A is matched with C, the score in
the third row and first column is added.
EXAMPLES
The following is the beginning of a sample matrix for DNA
sequence matching.
10
0 0
-2 0 10
0 0 0 0
0 0 0 0 0
0 0 0 0 0 0
-2 0 7 0 0 0 10
0 0 0 0 0 0 0 0
.
.
.
Looking at the matches for G in the seventh row, the match G
-A has score -2, G-C has score 7, and G-G has score 10.
A full DNA scoring matrix for use with Genbank, for example,
should have entries for scoring N (any) and X (any protein).
Genbank encodes U in RNA as T; to be safe, if building a
matrix to compare RNA against a database, identical entries
should be made for U and T.
Alternatively, substitution matrices in BLAST format may be
used. Thus, as new matrices are made available in the
NCBI's blastapp distribution, they are supported by this
package.
SEE ALSO
seqaln-intro(1), mglobalS(1), mglobalD(1), mfitS(1),
mfitD(1), moverS(1), mlocalS(1), msrlocalS(1), mtrlocalS(1),
mpvlocalS(1).