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Old 02-04-2016, 08:11 AM   #1
Location: italy

Join Date: Sep 2010
Posts: 55
Default HMMER search with Conserved Domain Database

Dear All,

I am trying to identify conserved domains in my proteins. I would like to use the Conserved domain database (CDD) since I know it is the most complete, and I would like to the my search with hmmer that I know is very precise. In the ftp site of CDD I found theposition-specific scoring matrices (PSSMs) that can be used to create a database with makeprofiledb that can be scanned with rps-blast. However in order to use the database with hmmer I need the alignment files for the domains (something like clustalw, msf or so). Does anyone know where can I download the CDD in this format?

Thanks for your help
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