Re: BioJava translation
Andy Yates <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
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 <[email protected]> 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 - [email protected] > > 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 - [email protected] > 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 > ----------------------------------------------------------------------- -- 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 - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l