[Biojava-l] BioJava translation

[Andreas Prlic]

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.
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > 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/
>
>
>
>
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/biojava-l
>



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