<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Dear Leila,<div class=""><br class=""></div><div class="">I am afraid I can only help you with one of your question. Please find inline comment below.<br class=""><div><blockquote type="cite" class=""><div class="">On 16 May 2015, at 00:32, Leila Alieh <<a href="mailto:alieh.leila@gmail.com" class="">alieh.leila@gmail.com</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class=""><div class=""><div class=""><div class=""><div class=""><div class="">Hi all!<br class=""><br class=""></div>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 (<a href="http://lists.ensembl.org/pipermail/dev/2015-April/011013.html" class="">http://lists.ensembl.org/pipermail/dev/2015-April/011013.html</a>).<br class=""></div><br class=""></div>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.<br class=""><br class=""></div>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<br class=""></div></div></div></blockquote>We are doing our best, the Ensembl release 80 will be available before the end of the month. Just keep an eye on our <a href="http://www.ensembl.org/index.html" class="">ensembl website</a>, <a href="https://twitter.com/ensembl" class="">twitter</a>, <a href="http://www.facebook.com/Ensembl.org" class="">Facebook</a>, or <a href="http://www.ensembl.info/" class="">Ensembl blog</a>.</div><div><br class=""></div><div>Hope this helps,</div><div>Regards,</div><div>Thomas<br class=""><blockquote type="cite" class=""><div class=""><div dir="ltr" class=""><div class=""><br class=""></div>Thanks again!<br class=""></div>
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<div class=""><div class="" style="orphans: 2; widows: 2;">--</div><div class="" style="orphans: 2; widows: 2;">Thomas Maurel<br class="">Bioinformatician - Ensembl Production Team<br class="">European Bioinformatics Institute (EMBL-EBI)<br class="">European Molecular Biology Laboratory<br class="">Wellcome Trust Genome Campus<br class="">Hinxton<br class="">Cambridge CB10 1SD<br class="">United Kingdom</div></div>
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