[Bioperl-l] Parsing CDD Results?

Chris Fields cjfields at uiuc.edu
Sun Jan 21 21:12:26 EST 2007


On Jan 21, 2007, at 6:47 PM, Torsten Seemann wrote:

>>> Has anyone figured a good way to parse the results from NCBI's CDD
>>> database (i.e., http://www.ncbi.nlm.nih.gov/Structure/cdd/ 
>>> cdd.shtml )?
>
>> if you run it locally isn't it just RPSBLAST which *used* to be
>> parseable by Bio::SearchIO::blast - I am not sure now. or are you
>> talking about running it via web?
>
> Jason is correct.
>
> I run CDD searches locally via
> Bio::Tools::Run::StandAloneBlast->rpsblast() and parse the results
> with Bio::SearchIO. "rpsblast" comes with the standard BLAST package.
> You can download the CDD models already compiled too from NCBI's ftp
> site. RPS-BLAST runs very quickly too as their are only 12,000 models
> in the CDD database.
>
> --Torsten Seemann

I wasn't sure if he meant RPS-BLAST results or the data from the web  
page.

chris


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