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. -- Dr Leighton Pritchard MRSC D131, Plant Pathology Programme, SCRI Errol Road, Invergowrie, Perth and Kinross, Scotland, DD2 5DA e:lpr...@scri.ac.uk w:http://www.scri.ac.uk/staff/leightonpritchard gpg/pgp: 0xFEFC205C tel:+44(0)1382 562731 x2405 ______________________________________________________ SCRI, Invergowrie, Dundee, DD2 5DA. The Scottish Crop Research Institute is a charitable company limited by guarantee. Registered in Scotland No: SC 29367. Recognised by the Inland Revenue as a Scottish Charity No: SC 006662. DISCLAIMER: This email is from the Scottish Crop Research Institute, but the views expressed by the sender are not necessarily the views of SCRI and its subsidiaries. This email and any files transmitted with it are confidential to the intended recipient at the e-mail address to which it has been addressed. It may not be disclosed or used by any other than that addressee. If you are not the intended recipient you are requested to preserve this confidentiality and you must not use, disclose, copy, print or rely on this e-mail in any way. Please notify postmas...@scri.ac.uk quoting the name of the sender and delete the email from your system. Although SCRI has taken reasonable precautions to ensure no viruses are present in this email, neither the Institute nor the sender accepts any responsibility for any viruses, and it is your responsibility to scan the email and the attachments (if any). ______________________________________________________ _______________________________________________ Artemis-users mailing list Artemis-users@sanger.ac.uk http://lists.sanger.ac.uk/mailman/listinfo/artemis-users
