what are the differences between an hmmscan and a Pfamscan against PfamA?

Question

[dago]

I am comparing the results of an hmmscan and a Pfamscan done agianst PfamA.

I understand that the Pfamscan used as default a bit more stringent values, and I think that this might explain the lower number of hits I get with it.

So in theory if I set the limit for bit score and E value in both scripts I should get the same results. Is there any other difference that I am missing?

Answer 1

[venu]

As far as I know 'hmmscan', mainly used to map the HMM profile of a particular protein family to a specific protein sequence to know the domains present in the protein sequence. 'Pfamscan' which is mainly used to search a fasta sequence against a library of pfam HMM.

[GouthamAtla]

The question is not "what is the difference between hmmscan and pfamscan" and I am sure you just copy pasted the line "PfamScan is used to search a FASTA sequence against a library of Pfam HMM." from this link http://www.ebi.ac.uk/Tools/pfa/pfamscan/

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