[Bioperl-l] Parsing CDD Results?

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Sun Jan 21 19:47:32 EST 2007


> > 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


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