Using HMMer to emit and align sequences

All HMM models can not only parse sequences but they can also ``emit'' or produce sequences according to their probabilities. We'll use this to create a simulated dataset of 49 sequences, which we will then practice aligning to the model. Then we'll try making a weblogo.

1. Emit sequences accoording to the model using ehmmemit.
   % ehmmemit -number 40 ATP_bind_2_fs.hmm
   
2. Edit the first sequence with a random legal peptide randomly inserted into the sequence.
3. Align the sequences to the model using hmmalign:
   % ehmmalign ATP_bind_2_fs.hmm
   
4. Inspect the alignment with less. Can you find your insertion? what does it look like?
5. Convert the alignment with sreformat
   % sreformat a2m <alignment> > atp.fas
   
6. Make a weblogo. select ``multiline.'' Can you see the P-loopE motif?