hmmsearch to show all sequences

Question

[srx3001]

Hello all,

I am using hmmsearch to go over a small database of peptides (basically just a multifasta file) to search with certain hmmprofile's. Now that is all working great, but since I am visualizing the data using plots - like an hmm score for each hit compared to function of the peptide I need something else.

I am curious if its possible to show ALL sequences from the multifasta file instead of just the ones it "hits". If I set the E-value to +100 (from the default inclusion of 0.01) it still only shows only a fraction of the sequences. It would be fine even if the score isn't informative , I would just like to have an overview since this was asked of me in the lab.

Basically my plot would have a couple of peptide functions plotted on Y-axis, as integers (cathegories) and HMMscore would be on X-axis. So far I was only able to get the hmmscore for 120/400 of my peptides when I run the profile for a "general sequence" of the family.

Appreciate all the help

[jscience]

I ran into the same problem too. Does anyone have a solution to this?

Answer 1

[jscience]

I think I figured it out. It can be done by turning off the nobias filter (with the --nobias option).