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InterProScan and HMMER - different results

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:

./interproscan.sh -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!

interproscan hmmer pfam
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updated by owen.donohoe • owen.donohoe • written by yp19 yp19

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.

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written by h.mon h.mon

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?

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written by Asaf Asaf

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)

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written by yp19 yp19

On this basis, you should be able to reduce the correction that the inerproscan results are subjected to by confining your search to pfam libraries only ?

for example
./interproscan.sh -appl Pfam -i /path/to/sequences.fasta -f tsv

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written by owen.donohoe • owen.donohoe

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.

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written by h.mon h.mon

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