BJ3 should be replacing most sequence operations with string operations, making the whole thing much faster.
On 13 Oct 2010, at 12:15, Pjotr Prins wrote: > I am using biojava-1.7.1 nucleotide -> amino acid translation. It is > rather slow. In fact, the biopython equivalent in native Python is > twice as fast. EMBOSS is again magnitudes faster. I am using > something like > > rna = RNATools.createRNA(nucleotides); > aa = RNATools.translate(rna); > > Embarrassingly, even the R version is faster in the GeneR module, as > it uses a C module. > > I have a feeling this has to do with typed object creation at every > level, whereas Python and others uses plain character Strings. > > Any plans for speeding this up on the JVM? > > Pj. > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland, BSc MBCS Operations and Delivery Director, Eagle Genomics Ltd T: +44 (0)1223 654481 ext 3 | E: [email protected] http://www.eaglegenomics.com/ _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
