[Biojava-dev] Code Update

[Andy Yates]

Hi Mark,

I thought that there had been some cases of Valine in bacteria not  
being modified but that said it's probably me mis-understanding what  
the other person was saying :). However there is the in-flexibility in  
other resources/programs which can throw the toys out of the pram the  
moment they are presented with a peptide not starting with M.

What I was thinking is to either have this option available (much in  
the same way I've got stop codon trimming working) or using the  
planned edit capability. If I do put the optional translation as a  
boolean for the moment then that bit becomes a bit more feature  
complete and then a better solution can be applied later on :).

Anyway next on the hit list I think is locations ....

Andy

On 6 Feb 2010, at 15:45, Mark Schreiber wrote:

> 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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>> biojava-dev at lists.open-bio...
>>
>

-- 
Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/