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
