I am working on a homework assignment for a course I am taking. One of the question I am struggling to figure out for myself. What I have done so far is built a HMM model from a sequence with hmmbuild. Here is a short section of that hmmfile as viewed in my text editor
HMMER3/f [3.2.1 | June 2018]
NAME HH
LENG 234
ALPH amino
RF no
MM no
CONS yes
CS no
MAP yes
DATE Thu Feb 7 15:13:59 2019
NSEQ 4
EFFN 1.277344
CKSUM 332499440
STATS LOCAL MSV -10.4404 0.70356
STATS LOCAL VITERBI -11.2264 0.70356
STATS LOCAL FORWARD -5.0763 0.70356
HMM A C D E F G H
m->m m->i m->d i->m i->i d->m d->d
COMPO 2.41584 4.38536 2.97717 2.73283 3.39075 2.69139 3.72874
2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494
0.01974 4.33061 5.05296 0.61958 0.77255 0.00000 *
1 1.69017 4.39481 4.54757 4.02379 3.67877 4.14409 4.71397
2.68618 4.42225 2.77519 2.73123 3.46354 2.40513 3.72494
0.01974 4.33061 5.05296 0.61958 0.77255 0.48576 0.95510
Now for my assignment, we have to find the probability of emitting the first letter in our consensus sequence, transitioning to a match state, an insert state, and a delete state. I know that the decimal values represent negative log probabilities, but I'm a little confused as to what the first letter in the sequence would be, and whether or not it would be COMPO or 1.
I'm reasonably sure in order to find the probability of match, insert, and delete all I have to do is exponentiate the first row of values in section one under m->m, m->i, and m->d, (correct me if I'm wrong), but how do I find out what the probability of emitting the first letter in my consensus sequence?
