[BioRuby] CDART BioRuby
Sharvari Gujja
sgujja at broad.mit.edu
Thu Apr 10 18:20:26 UTC 2008
Hi,
I am trying to use NCBI CDART( Conserved Domain Architecture Retreival
Tool ) to analyze multiple protein sequences in fasta format.
CDART assigns domains based on RPS Blast so this is what I intend to do
in bioruby:
1. Take the input protein sequences file in fasta format .
2. Do RPS Blast for each sequence using Bio::Blast class
- I still have to look into it.
3. From the output get the pssm/cd id to efetch the cdd page from ncbi.
-This is where I need help.Is there a class in Bioruby which I
can use to retrieve the cdd page?
You can try an example : cd00066 to see how the output looks like (
search under Conserved Domain Database)
Appreciate any help.
Thanks
S
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