Question: InterProScan and HMMER - different results
gravatar for yp19
15 months ago by
yp1960 wrote:

Hi all!

I've run both InterProScan and HMMER because im interested in pfam hits for a set of proteins. Interproscan was run like so:

./ -i my_prot.faa -f tsv

and then i filtered the results for pfam hits with E value < 0.001

HMMER was run like so:

hmmscan --tblout hmmer_result.txt -E 0.001 Pfam-A.hmm my_prot.faa

I compared the outputs and for some reason, InterProScan finds less proteins with pfam hits than HMMER (approximately 150 proteins less). I checked and they are both using the most recent pfam database (32.0) so I'm not sure why this could be happening. Any ideas ?

Thank you!

pfam hmmer interproscan • 491 views
ADD COMMENTlink modified 12 months ago by h.mon31k • written 15 months ago by yp1960

Do you know what is the exact HMMER command InterProScan is using? Do you know if / how InterProScan filters input and output? You may have to dig InterProScan logs to find out these details.

ADD REPLYlink written 15 months ago by h.mon31k

Thank you. No I do not know the exact command. I figured the output was not filtered since I have some large evalues (e.g. 40). Do you know where I can find these logs? I made it this far but i'm not sure where to go from here.

ADD REPLYlink written 15 months ago by yp1960

My guess is that the multiple hypotheses correction is different, probably interproscan scans more profiles and has a more profound correction. Can you validate the correspondence between the e-values? Are you loosing the high e-value results?

ADD REPLYlink written 15 months ago by Asaf8.4k

Thank you for the suggestion. Yes it looks like I am losing the high e-value results. although, there are only 30 of these proteins with large (>0.001) evalues and I am missing 150 proteins in total (in comparison to HMMER)..... Perhaps there is some filtering on the evalues that interproscan is doing (after multiple testing)

ADD REPLYlink modified 15 months ago • written 15 months ago by yp1960

Please do not delete posts. The purpose of this site is two-fold: more immediately, to help people with their questions; but on the long run, to serve as a repository of knowledge. The second purpose is defeated if people delete their questions.

ADD REPLYlink written 12 months ago by h.mon31k
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: 2251 users visited in the last hour