Hi Jack, Scott, This does look to be the best solution at the moment and appears that may have been a quick solution here in the past.
I will look at implementing this for the next release. This may take the form of an extra check box on the ³minimum open reading frame² window, so that Artemis knows to use the ends of the sequences in multiple fasta files. Regards Tim On 25/6/07 17:02, "Scott Beatson" <[EMAIL PROTECTED]> wrote: > Hi Jack, > > A quick solution is to insert a short sequence containing stop codons in all > six reading frames in between every contig sequence in your fasta file. I > agree it would be nice to have this as an artemis feature. > > Cheers > Scott > > On 26/06/2007, at 1:03 AM, Jack van de Vossenberg wrote: > >> Dear all, >> >> I am not sure if this came up already, but I have a question. If it cannot be >> done I'll make it a feature request. >> >> We have a 454 genome sequence, which is fragmented into many contigs. We used >> a fasta file of all contigs to start genome annotation. Artemis was used to >> determine ORFs. >> Unfortunately some ORFs cross the contig border to the next (random position) >> contig. This makes annotation, especially automated blasts, more difficult, >> and sometimes we miss info. Is there a way to tell Artemis not to cross >> contig borders while defining ORFs? If it is not possible I request an option >> for this for future releases ;) I think that more and more people will have >> fragmented genome data for quick/early screening. >> >> Cheers, Jack >> >> _______________________________________________ >> Artemis-users mailing list >> [email protected] >> http://lists.sanger.ac.uk/mailman/listinfo/artemis-users >> > > > --- > > Scott Beatson PhD > NHMRC Howard Florey Research Fellow > School of Molecular and Microbial Sciences > University of Queensland > Brisbane QLD 4072 > Australia > > Tel: +61 7 33654863 > Fax: +61 7 33654699 > > > > > > > > _______________________________________________ > Artemis-users mailing list > [email protected] > http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
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