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
