[Biojava-l] BioJava translation

Richard Holland holland at eaglegenomics.com
Wed Oct 13 11:27:05 UTC 2010

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.
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Richard Holland, BSc MBCS
Operations and Delivery Director, Eagle Genomics Ltd
T: +44 (0)1223 654481 ext 3 | E: holland at eaglegenomics.com

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