[Biojava-l] BioJava translation

Pjotr Prins pjotr.public23 at thebird.nl
Wed Oct 13 18:17:12 UTC 2010

I think it is a good idea. From a purist point of view you may object
(it is not biological), but most libraries do exactly that.

If direct translation gets it down to 8sec, we may well half that
with further tweaking.


On Wed, Oct 13, 2010 at 01:16:01PM -0400, Scooter Willis wrote:
> The Biojava3 has an additional validation layer and object creation going
> from DNA sequence to RNA sequence and then using the appropriate translation
> rules to return a protein sequence. Could be easily twice as fast if you
> went from DNA sequence to ProteinSequence which would put it at 8 seconds.
> We are going to carry a performance penalty setting everything up as a
> proper object versus doing a simple String to String translation.

More information about the Biojava-l mailing list