Hi Andy, I am actually counting codons via 6 ORFs translations. I am working on ±100.000 seq/run => 600.000 ORFs to check. So, performance is an issue for my job.
I am just wondering if counting Codons directly on NT seq (both strand) will be faster vs translation + AA counting. Regards, khalil On 21 Apr 2011, at 13:40, Andy Yates wrote: > 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
