Hi Betina,
If you're fetching 454 reads, it doesn't surprise me that it is rather
slow, since you'll have a lot of read to fetch. This is probably due
to the highly normalized nature of Chado. I'd imagine that anything
that is reading off the database directly and fetching so many
results (which causes a large number of joins to be made) will be
slow. Perhaps you could look into using materialized views, which
I believe the most current release of Chado supports. However,
Apollo's code would have to be updated to support these views.
Cheers,
Ed
On Thu, 24 Sep 2009, Betina Porcel wrote:
Hi there!
Today, I'm have some doubts concerning Apollo's performance.
Here my problem:
still using Apollo1.10.0 connected to a Chado DB
I've been testing the time Apollo needs to open a genomic region, and here
the result:
when trying on a region with no much stuff (some repeats and abInitio
results, always on the results side), Apollo is taking more less 30 seconds
to open a 5kb region. But! when trying on a region where all the resources
are present (results of proteins alignements, ESTs, and mostly 454 reads!)
opening 10kb is taking me 5 minutes.
I know that the more results you have in the database, the longer the time
Apollo takers to open your genomic region, is the performance I'm getting
"normal"? What about your experiences?
We'll be starting a manual curation projet soon, and I'm pretty worried about
the time that'll take for our colleaugues to open Apollo!!!!
Any suggesstions?
Thanks a lot!!!!
Betina
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