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: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] > Sent: Sunday, 13 July 2003 10:04 p.m. > To: [EMAIL PROTECTED] > 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 > > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
