Hi Andy - hope you're keeping well !
Mungo is progressing really well with Ensembl/Jalview integration, and
is looking for some complicate gene models that we can use to test
Jalview's import and display of aligned transcripts & products.
Are there sets of pathological gene models the Ensembl team use ?
Jim
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Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk
Hi Mattieu - good to have you on board!
Mungo (cc'ed) is currently working on an Ensembl gene importer. At some point soon he'll be downloading alignments from Compara - but before that, we're just trying to make sure we have the Genome->Transcript(s)->Product(s) mappings correct for all cases.
I seem to remember at some point in a conversation with someone related with Ensembl (perhaps Mark McDowall, but could easily have been Dan Bolser) that before every ensembl release, some of the particularly difficult gene models were checked to make sure that they were being handled correctly by the system. Of course - I could also have imagined this 
Do you have a list of 'problem' genes where the architecture is complex and/or diverse ? I suppose we could hunt for these ourselves but if you have some examples handy that would be great!
Jim.
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On 01/03/2016 17:51, Andrew Yates wrote:
Hi Jim
It's good to hear from you. Glad to hear that the integration is going well! I've included Matthieu who is our compara project leader in Ensembl who can advise. Pathological genes however my first instinct goes to something like Titin. Or possibly one of the olfactory receptors. Olfactory might be especially good due to the families in that set.
If there's anything else we can do to help you out or you need from our interfaces just let me know and I can always get you or anyone on Jalview in-touch with the right person here
Andy
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Andrew Yates - Genomics Technology Infrastructure Team Leader
The European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus
Hinxton, Cambridge
CB10 1SD, United Kingdom
Tel: +44-(0)1223-492538
Fax: +44-(0)1223-494468
Skype: andy.yates.ebi
http://www.ebi.ac.uk/
http://www.ensembl.org/
> On 1 Mar 2016, at 10:56, Jim Procter <jprocter@compbio.dundee.ac.uk> wrote:
>
>
> Hi Andy - hope you're keeping well !
>
> Mungo is progressing really well with Ensembl/Jalview integration, and
> is looking for some complicate gene models that we can use to test
> Jalview's import and display of aligned transcripts & products.
>
> Are there sets of pathological gene models the Ensembl team use ?
>
> Jim
>
> --
> -------------------------------------------------------------------
> Dr JB Procter, Jalview Coordinator, The Barton Group
> Division of Computational Biology, School of Life Sciences
> University of Dundee, Dundee DD1 5EH, UK.
> +44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk
>
--
-------------------------------------------------------------------
Dr JB Procter, Jalview Coordinator, The Barton Group
Division of Computational Biology, School of Life Sciences
University of Dundee, Dundee DD1 5EH, UK.
+44 1382 388734 | www.jalview.org | www.compbio.dundee.ac.uk