Re: BioJava translation

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

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