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:



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!

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