There will be a performance hit but you'll be rewriting the translation code so maybe the speed reduction isn't worth the recoding task. Give it a benchmark before recoding. I can't remember the exact speed but it isn't too slow
Andy Khalil El Mazouari <[email protected]> wrote: >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
