I am experimenting with the SearchProfile sample app. I am confused about how the "StoppingCriteria" is to be used to specify termination conditions for the training algorithm. In my testing, most fasta protein sequences cause the system to "hang" after one cycle of training. Very simple sequences work (i.e. continue on through the 5 cycles specified in the test app). Can anyone offer a ray of enlightment here? Also: I see no provision for specifying pseudocounts in constructing the HMM model from the primary data. Is this correct? R.McIntosh _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
