[Bioperl-l] SearchIO: write/read database

Jason Stajich jason at bioperl.org
Thu May 22 01:45:10 EDT 2008

Do you already have a database schema structure designed for storing  
BLAST/similarity results?

As it tries to say in the quote, this would be possible, but as it  
stands there is no "BLAST result database" that is part of BioPerl at  
this time.  It would be a relatively straight-forward solution, but I  
don't know if it makes more sense to try and store things in a  
database schema like Chado so that this is not Yet-Another-Standalone- 

On May 20, 2008, at 1:09 AM, Chu, Roy wrote:

> Hi,
> I tried a mailing-list and module search, but I couldn't find what  
> I was looking for--but I know it's there.
> On the bioperl page (http://www.bioperl.org/wiki/ 
> HOWTO:SearchIO#Writing_and_formatting_output) it says:
> "If your data is instead stored in a database you could build the  
> Bio::Search objects up in memory directly from your database and  
> then use the Writer object to output the data."
> I want to write/read BLAST results to a database w/o having to  
> write to files or parse any xml.  Can someone direct me to any  
> available module(s) that will help me in my endeavor?
> Thanks in advance,
> Roy
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