Hi,
If I create a uniform protein distribution and check the emission
probabilities, I find that they are set to 1/21 rather than 1/20...
Henry Romijn
FiniteAlphabet emissionAlpha =
(FiniteAlphabet) AlphabetManager.alphabetForName("PROTEIN");
ProfileHMM profile = new ProfileHMM(
emissionAlpha,
length,
DistributionFactory.DEFAULT,
DistributionFactory.DEFAULT,
name
);
ModelTrainer mt = new SimpleModelTrainer();
mt.registerModel(profile);
mt.setNullModelWeight(1.0);
// output
PRO 0.047619047619047596
ARG 0.047619047619047596
CYS 0.047619047619047596
GLU 0.047619047619047596
VAL 0.047619047619047596
GLY 0.047619047619047596
GLN 0.047619047619047596
HIS 0.047619047619047596
ASN 0.047619047619047596
THR 0.047619047619047596
SEC 0.047619047619047596
LYS 0.047619047619047596
PHE 0.047619047619047596
LEU 0.047619047619047596
ASP 0.047619047619047596
SER 0.047619047619047596
TRP 0.047619047619047596
MET 0.047619047619047596
TYR 0.047619047619047596
ALA 0.047619047619047596
ILE 0.047619047619047596
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