[Biojava-l] Error initializing uniform protein distribution

[Schreiber, Mark]

Hi -

This is because the Protein alphabet contains 20 amino acids and
Selenocystein (SEC). Which admitidly is a bit of a trap for people new
to BioJava (or people new to the Protein Alphabet).

It is not generally a good idea to use a Uniform protein distribution
(other than for testing) as you won't see anything like that in nature.

- Mark

> -----Original Message-----
> From: hlr02 at doc.ic.ac.uk [mailto:hlr02 at doc.ic.ac.uk] 
> Sent: Sunday, 13 July 2003 10:04 p.m.
> To: biojava-l at biojava.org
> Subject: [Biojava-l] Error initializing uniform protein distribution
> 
> 
> 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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