Hi Torsten Thanks for reporting this. The problem was that it was using the phase of the last exon (not the first) in the CDS features on the reverse strand. I have implemented a fix for this now and this is available from the development download section (Artemis version 14.1.1) on the home page:
http://www.sanger.ac.uk/resources/software/artemis/#development Regards Tim On 7/30/12 8:31 AM, "Torsten Seemann" <torsten.seem...@monash.edu> wrote: > Tim et al, > > I've just run some MAKER2 annotations on a small parasite genome > (eukaryotic)., producing a GFF3 file. About 70% of the genes have > phase=0 (GFF column 8), while 15% have phase=1 and 15% have phase=2. > Artemis seems to load it (mostly) fine, and puts > /codon_start=(phase+1) tags. > > However, when viewing, all the genes look fine on the +strand no > matter the phase, but the (some of the?) non-zero phase ones > (/codon_start 2 or 3) on the -strand seem to render incorrectly, with > the exons being out of frame. > > I've looked through the mailing list archives, and found one reference > to a similar problem, but it appeared to be resolved, but I've > reproduced it somehow. I'm using Artemis 14.0.11. I'm also getting > possibly related warnings - about 100 x "RANGE NOT FOUND xxxx..yyyyy". > > Any help appreciated! _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
