Downloading HMM profiles from Interpro

Question

[venuraherath]

Hi Folks,

Is there anyway to download HMM profiles used in Interpro Search? If it is not possible how can I retrieve SMART hmm profiles. I dont fine hmm profiles in their ftp site.

Thank in advance,

Venura

[ashish]

Do you want all the HMM profiles or some selected ones? Anyways, if you don't find them then you can download PSSMs from NCBI CDD and then use them to perform RPS-BLAST against your sequences.

[venuraherath]

Thank you Ashish. I want to use Domosaics program (combine domains, tree and alignment) unfortunately it no longer functional when it comes to Interproscan. Only work around is to get hmm profiles and do local search :( .

Answer 1

[Jean-Karim Heriche]

As far as I know, InterPro relies on protein signatures from databases in the InterPro consortium so you should search there. You may have to explicitly request the data if not available for download. If you want to search some sequences against InterPro signatures, you can use the InterProScan software.

[venuraherath]

Hi Jean-Karim, Thank you. I wrote to Protein families team at Interpro. They said download interproscan and there i will find the hmm signatures. It is a huge file and still downloading. Hopefully, HMMs will be there. Fingers crossed.