[Biojava-l] BioJava translation

[Scooter Willis]

Pjotr

What is an extra 8 seconds among friends if you know you are going to get
the correct answer and you can change the rules if needed!!!

Are you parsing the C.elgans genome or DNA representation of each protein in
the C.elgans genome?

If you take out the println statement that will help speed things up a
bunch. Java System.out is always slow.

I am checking on the problem with upper case. That shouldn't be an issue.

Thanks

Scooter


On Wed, Oct 13, 2010 at 2:17 PM, Pjotr Prins <pjotr.public23 at thebird.nl>wrote:

> 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.
>
> Pj.
>
> 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.
>
>