[Bioperl-l] Blast Results IO to Local RDBMS
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?
Dept. of Human Genetics
University of Utah
Salt Lake City, UT
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