Question: HMMER search on conserved domain database
gravatar for salvocamiolo
4.3 years ago by
salvocamiolo20 wrote:

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


hmmer cdd domains forum • 1.6k views
ADD COMMENTlink modified 4.3 years ago by Jean-Karim Heriche22k • written 4.3 years ago by salvocamiolo20
gravatar for Jean-Karim Heriche
4.3 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche22k wrote:

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

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

ADD COMMENTlink modified 4 months ago by RamRS27k • written 4.3 years ago by Jean-Karim Heriche22k
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