[Biojava-l] BioJava translation

Pjotr Prins pjotr.public23 at thebird.nl
Wed Oct 13 11:15:41 UTC 2010

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? 


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