Question: hmmsearch to show all sequences
gravatar for srx3001
3.7 years ago by
srx300110 wrote:

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

hmmer hmmsearch multifasta • 1.2k views
ADD COMMENTlink modified 12 months ago by jscience0 • written 3.7 years ago by srx300110

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

ADD REPLYlink written 12 months ago by jscience0
gravatar for jscience
12 months ago by
jscience0 wrote:

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

ADD COMMENTlink modified 12 months ago • written 12 months ago by jscience0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1459 users visited in the last hour