Your results are very fast. I am now using the latest versions including biojava-1.3pre4-jdk14.jar, etc. and PostgreSQL 7.3.3 on Linux 2.4.20.
It needs 30 seconds to run your filter on my system. Cheers, George > -----Original Message----- > From: Simon Foote [mailto:[EMAIL PROTECTED] > Sent: 09 June 2003 13:02 > To: Y D Sun > Cc: [EMAIL PROTECTED] > Subject: Re: [Biojava-l] Different implementation of Sequence? > > > Hi George, > > 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] > > > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
