[ensembl-dev] protein coordinates of domains and exons

Thomas Maurel maurel at ebi.ac.uk
Mon May 18 13:35:00 BST 2015

Dear Leila,

I am afraid I can only help you with one of your question. Please find inline comment below.
> On 16 May 2015, at 00:32, Leila Alieh <alieh.leila at gmail.com> wrote:
> Hi all!
> I have a list of genomic coordinates of exons and I want to transform them into protein coordinates of the different protein isoforms these exons belong to. Moreover I want to find the protein coordinates of the domains of these proteins, and then overlap the 2 sets of information to find exons which encode for protein domains. For what I read the (only?) way to do so is to use the Perl API of ensembl, and in particular  I should use TranscriptMapper and ProteinFeauture, right? I read the the tutorial and the documentation but I still find it very difficult to understand the API and I don't knowhow to write the code in a way to restrict the query only to my list of exons/proteins. Could you please show me some examples? In particular I'd like to know what Greg did to find the protein coordinates of the protein domains (http://lists.ensembl.org/pipermail/dev/2015-April/011013.html <http://lists.ensembl.org/pipermail/dev/2015-April/011013.html>).
> Thank you in advance and I apologize if I did some mistake in the thread, it's the first time that I'm using the ensembl mailing list.
> P.S. Please, please, please, make the protein coordinates accessible in Ensembl gene mart as soon as possible, it would save a lot of work/time
We are doing our best, the Ensembl release 80 will be available before the end of the month. Just keep an eye on our ensembl website <http://www.ensembl.org/index.html>, twitter <https://twitter.com/ensembl>, Facebook <http://www.facebook.com/Ensembl.org>, or Ensembl blog <http://www.ensembl.info/>.

Hope this helps,
> Thanks again!
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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Cambridge CB10 1SD
United Kingdom

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