Here's the result of tests with my database searcher webapp against several genomes individually. Unfortunately, it's not a pure CDS search as I recently modified the app to also return the DNA sequence for the feature, so that adds additional time depending upon the size of the genome.
The search gene is dnaA, the search filter consists of:
FeatureFilter ff1 = new FeatureFilter.ByType("CDS");
FeatureFilter ff2 = new FeatureFilter.AnnotationContains("gene", geneId);
FeatureFilter ff3 = new FeatureFilter.AnnotationContains("ibs_id", geneId);
FeatureFilter ff5 = new FeatureFilter.AnnotationContains("gene_id", geneId);
FeatureFilter ff4 = new FeatureFilter.Or(ff2, ff3);
FeatureFilter ff6 = new FeatureFilter.Or(ff4, ff5);
FeatureFilter ff7 = new FeatureFilter.And(ff1, ff6);
FeatureHolder fh = seq.filter(ff7, false);
Bacteria Search Time E.coli K12 6 seconds H. influenzae 4 seconds C. jejuni 6 seconds H. pylori J99 6 seconds
Note: Which version of the biosql schema are you using and which version of biojava
Regards, Simon
Y D Sun wrote:
-----Original Message-----
From: Simon Foote [mailto:[EMAIL PROTECTED] Sent: 05 June 2003 12:59
To: Y D Sun
Cc: [EMAIL PROTECTED]
Subject: Re: [Biojava-l] Different implementation of Sequence?
Just to add my 2 cents worth.
I'm using the latest version of the BioSQL schema within MySQL and the filters are quite fast. On a database containing 18 complete bacterial genomes, fetching a given gene by name which uses a combination of 5 filters in my case, takes approx. 1-2 seconds.
Simon,
Have you tried to filter all CDS sections of a complete bacterial
genome? In my experience with PostgreSQL, it takes only a few seconds to
filter a simple feature. However, it needs more than one minute to
filter thousands of CDS's in a genome.
George
-- Bioinformatics Specialist Institute for Biological Sciences National Research Council of Canada [T] 613-990-0561 [F] 613-952-9092 [EMAIL PROTECTED]
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