[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- 
Database-Schema-in-Informatics.

-jason
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
>
>
>
> ---------------------------------------------------------------------
>
> SECURITY/CONFIDENTIALITY WARNING:
> This message and any attachments are intended solely for the  
> individual or entity to which they are addressed. This  
> communication may contain information that is privileged,  
> confidential, or exempt from disclosure under applicable law (e.g.,  
> personal health information, research data, financial information).  
> Because this e-mail has been sent without encryption, individuals  
> other than the intended recipient may be able to view the  
> information, forward it to others or tamper with the information  
> without the knowledge or consent of the sender. If you are not the  
> intended recipient, or the employee or person responsible for  
> delivering the message to the intended recipient, any  
> dissemination, distribution or copying of the communication is  
> strictly prohibited. If you received the communication in error,  
> please notify the sender immediately by replying to this message  
> and deleting the message and any accompanying files from your  
> system. If, due to the security risks, you do not wi!
>  sh to receive further communications via e-mail, please reply to  
> this message and inform the sender that you do not wish to receive  
> further e-mail from the sender.
>
> ---------------------------------------------------------------------
>
>
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l



More information about the Bioperl-l mailing list