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 >> >> >> >> _______________________________________________ >> Biojava-l mailing list - [email protected] >> http://lists.open-bio.org/mailman/listinfo/biojava-l > > -- > 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/ > > > > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
