On Wed, Oct 13, 2010 at 12:15 PM, Pjotr Prins <[email protected]> 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.
Actually (assuming you are not explicitly using strings), Biopython would also be using objects for each sequence, which does impose a speed penalty. Peter _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
