[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(

Re: [Biojava-l] Error initializing uniform protein distribution

On Sun, 13 Jul 2003 [EMAIL PROTECTED] wrote: > 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 > That's because the alphabet includes selenocysteine which leads to a total count of

RE: [Biojava-l] bytecode jar biojava-live build wierdness...

Bad Matthew, breaking CVS again :) > -Original Message- > From: David Huen [mailto:[EMAIL PROTECTED] > Sent: Saturday, 12 July 2003 1:03 p.m. > To: DeAngelo Lampkin > Cc: Biojava-L (E-mail) > Subject: Re: [Biojava-l] bytecode jar biojava-live build wierdness... > > > On Fri, 11 Jul 2003

RE: [Biojava-l] Error initializing uniform protein distribution

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 wo