Question: HMMER search on conserved domain database
0
gravatar for salvocamiolo
21 months ago by
salvocamiolo10
Italy
salvocamiolo10 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 • 704 views
ADD COMMENTlink modified 21 months ago by Jean-Karim Heriche13k • written 21 months ago by salvocamiolo10
0
gravatar for Jean-Karim Heriche
21 months ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche13k 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 reformat.pl script from here.
 

ADD COMMENTlink modified 21 months ago • written 21 months ago by Jean-Karim Heriche13k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1669 users visited in the last hour