[Biojava-l] structure alignment seems slow ...

[Andreas Prlic]

The old StructurePairAligner is unpublished and is probably slower
than the CE and FATCAT implementations. Try e.g. CE:

http://biojava.org/wiki/BioJava:CookBook:PDB:CE_Algorithm

Andreas



On Wed, Jan 19, 2011 at 2:49 PM, Jay Vyas <jayunit100 at gmail.com> wrote:
> Hi guys :
>
> The following code snippet, for two 150 amino acid proteins, is taking a
> somewhat long time, that is, well over 4  minutes, ....
>
>        long t=(System.currentTimeMillis());
>        StructurePairAligner aligner = new StructurePairAligner();
>        aligner.align(s1, s2);
>        aligner.setDebug(false);
>        System.out.println("time = " + (System.currentTimeMillis()-t)/1000+"
> sec");
>
> Strangely, Im running biojava on a 2x28 GHz Quad Core Intel Xeon chip, Mac
> OS 10.5.8, with aggressiveheap enabled, and 6 Gigs of RAM.
> This suprises me since the tests on the biojava wiki page for structural
> alignments seem to be quite efficient.
>
> --
> Jay Vyas
> MMSB/UCHC
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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