[ensembl-dev] protein coordinates of domains and exons

[Leila Alieh]

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).

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

Thanks again!
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