[Bioperl-l] Optimizing Bioperl db queries

Law, Annie Annie.Law at nrc-cnrc.gc.ca
Fri Aug 27 14:07:30 EDT 2004


I would appreciate help on the following.  I am trying to create an
annotation database and
Am trying to obtain from starting point clone ids and end point being
Locuslink id's and GO terms, gene symbols, gene names.

I have loaded my bioperl-db database with scripts such as load_ontology.pl
and loadseqdatabase.pl.
I am using VB and sql queries to pull out the data.  

I am able to get the data that I want however it is quite slow.  I have 15
clone ids and it takes about 30s to retrieve
The data that I would like to get.  
This is only my test case and there may be times that my input will be 15000
Aside from the bioperl tables I have some other tables that are used.  So in
total I have about 9 sql queries
And some of these queries are in loops.

How are the people out there optimizing the set of queries to get a faster
I have indexed some tables but I think there is a better solution.

Thanks very much,

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