HMMER search on conserved domain database

Question

[salvocamiolo]

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 the position-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

Answer 1

[Jean-Karim Heriche]

The CCD ftp site has the alignments in multi-fasta format in file fasta.tar.gz.

You can convert to another format using the reformat.pl script from here.