ALPHABET= alphabet log-odds matrix: alength= alength w= w row_1 row_2 ... row_w |
ALPHABET=followed by alphabet, a list containing the letters used in the motifs. The order of the letters in alphabet must be the same as the order of the columns of scores in the motifs. The order need not be alphabetical and case does not matter, but there should be no spaces in alphabet. The letters in alphabet must be a subset of either the IUB/IUPAC DNA (ABCDGHKMNRSTUVWY*-) or protein (ABCDEFGHIKLMNPQRSTUVWXYZ*-) alphabets. DNA alphabets must contain at least the letters ACGT. Protein alphabets must contain at least the letters ACDEFGHIKLMNPQRSTVWY. All other letters in the alphabets are optional. If any of the optional letters are missing from alphabet, MAST automatically generates scores for them by taking the weighted average of the scores for the letters which the missing letter could match. (The weights are the frequencies of the replaced letters in the appropriate non-redundant database.) Replacements for the optional letters are given in the following table.
optional letter | matches | |
---|---|---|
DNA | protein | |
B | CGT | DN |
D | AGT | |
H | ACT | |
K | GT | |
M | AC | |
N | ACGT | |
R | AG | |
S | CG | |
U | T | ACDEFGHIKLMNPQRSTVWY |
V | CAG | |
W | AT | |
X | ACDEFGHIKLMNPQRSTVWY | |
Y | CT | |
Z | EQ | |
* | ACGT | ACDEFGHIKLMNPQRSTVWY |
- | ACGT | ACDEFGHIKLMNPQRSTVWY |
ALPHABET= ACGT log-odds matrix: alength= 4 w= 9 -4.275 -0.182 -4.195 1.408 -4.296 -1.487 1.880 -0.816 -2.160 -1.492 -4.171 1.474 -0.810 -4.076 1.872 -2.164 1.537 -1.487 -4.195 -4.205 0.113 0.340 -0.237 -0.209 -0.454 0.923 0.390 -0.834 -1.336 -0.082 0.905 0.100 0.674 -4.183 0.130 -0.201 log-odds matrix: alength= 4 w= 6 -2.032 0.324 1.371 -0.781 -0.409 0.560 -0.250 0.119 -4.274 -0.519 -0.260 1.167 -2.188 2.300 -4.191 -2.465 1.265 -4.111 -0.267 -2.180 -1.977 2.158 -1.661 -2.071 |