Just to let the people now that this has been resolved. Leighton has tried this out the changes to Artemis and is so far pleased.
The Artemis code can now infer CDS and UTR features when the chado_infer_CDS_UTR option is set to yes. The changes are now in the Artemis CVS. (There are instructions on how to download the code from CVS on the Artemis home page). You will need to edit etc/options to set: chado_infer_CDS_UTR=yes The updated documentation is in CVS as well under docs/chado/. This is also now available in the development version on the Artemis home page: http://www.sanger.ac.uk/Software/Artemis/#development -Tim On 6/8/09 12:10 PM, "Leighton Pritchard" <lpr...@scri.ac.uk> wrote: > Hi Tim, > > On 08/06/2009 12:00, "Tim Carver" <t...@sanger.ac.uk> wrote: > >> There were a couple of reasons why it was decided to store the gene models >> in that way in the Pathogen database here. People felt that they may want to >> annotate to a UTR and also in some ways it was a closer representation to >> how the standard Artemis would work with separate UTRs and CDS features. > > I'm not mad keen on the 'inference' model myself, though I think I can guess > why it was done (degrees of freedom and synchronising UTR/CDS annotation > changes). For my own purposes I'd rather have all features stored > explicitly. > >> However, I will now have a look at this so that Artemis can optionally work >> with this alternative representation and so that it correctly infers the >> UTRs. > > Thanks for looking into it - I hope it doesn't require too disruptive a > change. I think the best outcome - for me - would be to have Artemis exons > represent the exon in the db, and for CDS and UTR to be inferred as new > features in the gene model, with CDS locations corresponding directly to the > polypeptide. > > Thanks again, > > L. _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
