[Biojava-l] Codon count

[Khalil El Mazouari]

Thanks Andy,
it's the second option I am looking for.

Regards,
khalil



On 21 Apr 2011, at 13:23, Andy Yates wrote:

> Hi Khalil,
> 
> I'm not 100% sure what you want here. If you just want to know the potential number of codons on both strands of DNA then it would be (length / 3)*2. If what you are actually asking for is how many codons code for an amino acid then you would have to perform work similar to the transcription engine in BJ3. All codon tables are available from the IUPACParser class & then it would be up to you to use a WindowedSequence over the top of your NT sequence to get the windows or SequenceMixin.nonOverlappingKmers() which shortcuts the creation of the WindowedSequence.
> 
> Regards,
> 
> Andy
> 
> On 21 Apr 2011, at 11:36, Khalil El Mazouari wrote:
> 
>> Hi,
>> 
>> I am looking for a simple method or class to count the number of a specific AA codon on NT seq. Counting on both strands.
>> 
>> Any suggestion is welcome. 
>> 
>> Regards,
>> 
>> khalil
>> 
>> 
>> 
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> 
> -- 
> 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/
> 
> 
> 
>