[Biojava-l] BioJava translation

[Andy Yates]

I will try my best to

Andy

On 13 Oct 2010, at 16:42, Andreas Prlic wrote:

> 
> Hi Andy,
> 
> any chance to add some wiki documentation for this as well? Would be great....
> 
> Andreas
> 
> 
> On Wed, Oct 13, 2010 at 4:50 AM, Andy Yates <ayates at ebi.ac.uk> wrote:
> As of the moment there are the translation test cases which is the best documentation:
> 
> http://github.com/biojava/biojava/blob/master/biojava3-core/src/test/java/org/biojava3/core/sequence/TranslationTest.java
> 
> This hopefully will give you a good idea about how to go about it. I was managing over 1000 translations per second of BRCA2 going from mRNA to peptide with checks. YMMV but I hope this is a lot faster than what you're currently seeing.
> 
> Translation supports a lot of different modes with TranscriptionEngine being the place to configure this. The Javadoc should be good enough to help you through the different modes available
> 
> Andy
> 
> 
> On 13 Oct 2010, at 12:40, Pjotr Prins wrote:
> 
> > Great! You mean BJ3 translation should work? Do you have a short
> > example of use?
> >
> > Pj.
> >
> > On Wed, Oct 13, 2010 at 12:27:05PM +0100, Richard Holland wrote:
> >> BJ3 should be replacing most sequence operations with string operations, making the whole thing much faster.
> > _______________________________________________
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> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> 
> --
> Andrew Yates                   Ensembl Genomes Engineer
> EMBL-EBI                       Tel: +44-(0)1223-492538
> Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
> Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/
> 
> 
> 
> 
> 
> _______________________________________________
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> 
> 
> -- 
> -----------------------------------------------------------------------
> Dr. Andreas Prlic
> Senior Scientist, RCSB PDB Protein Data Bank
> University of California, San Diego
> (+1) 858.246.0526
> -----------------------------------------------------------------------

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/