Hi, I am a beginner in biojava as well bioinformatics. I hope you can advice on the obstacles I am facing now.
I am trying to follow your example about the profile HMM at http://www.biojava.org/docs/bj_in_anger/profileHMM.htm, and I try to fill in those missing codes that are required. And finally I got it running. The code has no problem running until BaumWelchTrainer. But there is an exception when I try to score the sequence and outputting the state path. I am not sure if the way I code the test sequence initialization is correct: ------------------------------------------------------ StatePath obs_rolls = dp.generate(18); SymbolList roll_sequence = obs_rolls.symbolListForLabel(StatePath.SEQUENCE); SymbolList[] sla = {roll_sequence}; ------------------------------------------------------ The exception says "Symbol d-1 not found in alphabet Transitions from d-1", which is at dp.generate(18). I appreciate if you can help me look into it. The source code & the input file is attached for your ref. And, what is dp.generate(int) means? If I have a number of variable length sequences, should I take the longest length of those sequences? or I am wrong totally about what it means? THANKS!! __________________________________ Do you Yahoo!? The New Yahoo! Shopping - with improved product search http://shopping.yahoo.com
>SEQ0 FPHFDLSHGSAQ >SEQ1 FESFGDLSTPDAVMGNPK >SEQ2 FDRFKHLKTEAEMKASED >SEQ3 FTQFAGKDLESIKGTAP >SEQ4 FPKFKGLTTADQLKKSAD >SEQ5 FSFLKGTSEVPQNNPE >SEQ6 FGFSGASDPG
PHMM.java
Description: PHMM.java
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