D'accord ;) Best
On Tue, Dec 6, 2011 at 9:20 AM, Hervé Ménager <hmena...@pasteur.fr> wrote: > Hi Andres, > From my point of view, it would do the job if I didn't have a _list_ of > genes as an input: I hence need to input a list of genes and get as an > output a list of the longest ORF computed for each gene. If I do this > directly with getorf and sizeseq, my understanding is that sizeseq won't > allow me to select the longest ORF for each input sequence. I can make the > loop myself, but I won't unless it is not ẗhere somewhere in EMBOSS ;). > Cheers, > Hervé > > > On 12/06/2011 01:53 PM, Andres Pinzon wrote: >> >> Herve, >> Have you tried using "getorf" and then "sizeseq"? >> I think it will work. Then you could get the first sequence from the >> output. >> >> Best, >> >> On Tue, Dec 6, 2011 at 6:11 AM, Jon Ison<ji...@ebi.ac.uk> wrote: >>> >>> A note of it is already on the SourceForge "Feature Requests" ... >>> >>> J:) >>> >>> >>> >>>> Hi Jon, >>>> >>>> That's exactly what would make me happy. Assuming it makes it easier for >>>> you if I formulate officially this request, where do I need to send the >>>> request? >>>> >>>> Hervé >>>> >>>> On 12/06/2011 12:00 PM, Jon Ison wrote: >>>>> >>>>> Hi Hervé >>>>> >>>>> Nothing in EMBOSS so far as I'm aware, but if all you want is for >>>>> checktrans to report the >>>>> longest >>>>> ORF then that should be an easy enough option to add. >>>>> >>>>> Cheers >>>>> >>>>> Jon >>>>> >>>>> >>>>>> Hi, >>>>>> I have been using transeq and checktrans to find ORFs in DNA >>>>>> sequences. >>>>>> I have an question regarding the selection of the ORFs in case >>>>>> checktrans finds multiple ones in the result of transeq: I would like >>>>>> to >>>>>> select the longest one automatically (assuming it is the correct one). >>>>>> Is there any existing tool in EMBOSS (or alternatively in any Bio* >>>>>> library) that does this job? >>>>>> Cheers, >>>>>> Hervé >>>>>> _______________________________________________ >>>>>> EMBOSS mailing list >>>>>> EMBOSS@lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/emboss >>>>>> >>>>> >>>>> >>>> >>> >>> >>> _______________________________________________ >>> EMBOSS mailing list >>> EMBOSS@lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/emboss >> >> >> >> > -- Andrés Pinzón _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss