Hi - How difficult would it be to make a markov model that emitted sequence from a state using a duration distribution. For Example in gene finding programs the model often loops over the coding state, unfortunately this means the probability of a certain length of sequence declines geometrically. In reality the length distribution of genes is a gamma distribution.
Without looking into the internals, I think you could sample the duration distribution to tell you how many times to sample the coding (or other) state. When doing the forward backward viterbi stuff I guess it would have to score the seqeunce by emission and rather than factoring in the transition probabilities it would look up the duration distribution instead. Now that we have the Integer sub alphabets this may not be too hard (I hope). - Mark Mark Schreiber PhD Bioinformatics AgResearch Invermay PO Box 50034 Mosgiel New Zealand PH: +64 3 489 9175 FAX: +64 3 489 3739 ======================================================================= 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
