[Biojava-dev] Code Update

[Mark Schreiber]

Hi Andy,

Great work!

Regarding the issue of non Met start codons such as TTG, biologically
speaking they are still translated as Met. fMet is the only tRNA that can
initiate. Presumably there is some flexibility in the recognition of the
start codon.

Maybe this is what you where aiming for but it would be good to have the
option of making the first codon translate to Met no matter what the codon.

Mark

On 06-Feb-2010 11:13 PM, "Andy Yates" <ayates at ebi.ac.uk> wrote:

Finally it's in. I've managed to get enough time to finish the transcription
code off. The main features of this check-in are:

* DNA -> RNA -> Codon -> Peptide translation
* Support for all IUPAC tables
* New views for reversing sequences & complementing them
* Windowed sequence views giving portions of a sequence as requested
* TranscriptionEngine & TranscriptionEngine.Builder deal with the business
of assembling the classes together as required
* Singletons provided from the classes they are in (e.g. IUPACParser has
one) *but* no class requires a singleton!
* Utilities for working with IO streams & classpath resources (useful for
testing)
* Test case shows 1000 translations of BRCA2 (from DNA) in 0.7seconds (on my
MacBook Pro; YMMV); test case will break if it takes longer than a second
** This is a vast improvement over my first attempt that had a rate of 1 per
second hence why that was not checked in

Limitations are:

* Not much checking WRT lengths of sequence given to the code; need a strict
& lenient mode
* Stop codon trimming controlled by a boolean
* No init-met translation (very important as some programs get a bit annoyed
if they're given a V as an initiator AA)
* Not sure if there is a way to ask if a codon is a start codon easily; I'm
sure it can be done just not as easily as we may want
* No way of modifying a badly translated peptide which we expect to badly
translate

However it's workable & means if you have a DNASequence technically you can
get a peptide by saying:

DNASequence s = getSeq();
ProteinSequence p = s.getRNASequence().getProteinSequence();

Now how's that for easy :)

Share & enjoy!

Andy


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