[Biojava-l] Problems with Baum-Welch training

Hi, I construct a profile HMM with randomized uniform distributions. I then train the model and, regardless of the training set I use, it ends up looking like this: - a 0.999 probability to go from one delete state to the next - roughly a uniform emission distribution for emission states (insert

[Biojava-l] Multiple sequence alignment

Hi, I am aligning a set of sequences to a profile HMM. I would like to convert the individual alignments into one (multiple sequence) alignment object. I tried to build a new map for my msa by retrieving the sequence symbollist from the statepaths and the sequence names. The problem with this a

[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(

[Biojava-l] Creating a dp object for a profile HMM (2)

Hi, I have narrowed down the problem in creating a dp object for a profile HMM to a possible bug in the code below from the DP class. I could really use some help here.. Thanks, Henry Romijn public static State[] stateList(MarkovModel mm) throws IllegalSymbolException, IllegalTransitionE

[Biojava-l] Creating a dp object for a profile HMM

Hi, After I have successfully created and initialized a profile HMM, I try to register the model with a new DP object as follows: DP dp = DPFactory.DEFAULT.createDP(profile); This causes the program to hang. Any ideas why this may not work? Thanks, Henry Romijn ___

[Biojava-l] Problems running SearchProfile demo

Hi, I can't get the SearchProfile demo to work and I have tried various input files. Is there a sample file available that will work so I can test if something else is wrong? Thanks, Henry Romijn Quoting [EMAIL PROTECTED]: > Hi, > > I have tried to run the SearchProfile demo with something

[Biojava-l] Problems running SearchProfile demo

Hi, I have tried to run the SearchProfile demo with something simple like: >a MGNA >b MGNA >c MGNA >d MGNA I use the ProfileHMM constructor that has a string as one of its parameters (instead of the deprecated one). There appear to be no problems in creating and initializing the ProfileHMM obj