[Bioperl-l] Blast Results IO to Local RDBMS

Barry Moore barry.moore at genetics.utah.edu
Wed Nov 3 14:10:13 EST 2004

I want to BLAST alot (100,000+) of ORFs and then save the results in a 
local relational database for periodic access later.  I was thinking 
something like Bio::SearchIO::Writer::HSPTableWriter to build table(s) 
for a "roll my own" schema and then  more code (either write it or find 
it) which pulls the search results back out of RDBMS and into 
Bio::Search object.  I recall about a month ago Jason replied to someone 
with a similar goal as follows:

>You will need to 
>build Bio::Search objects however from the DB - something that I am 
>sure has been done in part somewhere already.
>If someone gets this bit of to-from RDMBS code working for would be 
>really nice to have it in bioperl as just a simple component.   I know 
>lots of people have their own store-similarity-search-results schemas 
>out there, happy to see a Bio::Search serializiation layer written to 
>talk to these.

My question is:  Has anyone done this already? 



Barry Moore
Dept. of Human Genetics
University of Utah
Salt Lake City, UT

More information about the Bioperl-l mailing list