Hi Khalil, Then I think windowed sequence is the only way to go. Actually one particularly "interesting" idea has just sprung to mind. What if you translated the entire sequence in frame 1 forward & reverse? Then finding the amount of correct codons is a case of looking for amino acids which are not a stop or unknown amino acid.
Andy On 21 Apr 2011, at 12:37, Khalil El Mazouari wrote: > 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/ >> >> >> >> > -- 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
