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<div>Dear Matiss,</div>
<div><br>
</div>
<div>As mentioned in the posting guidelines linked at the bottom of
every dev message and sent to new subscribers to the list, Ensembl
provides user support both via this list and via
<a class="moz-txt-link-abbreviated" href="mailto:helpdesk@ensembl.org">helpdesk@ensembl.org</a> and we ask users to please not send the same
issue to both dev and helpdesk. </div>
<div><br>
</div>
<div>All of the questions eventually come to the same set of people
and it is generally a better use of time to answer the questions
only once. I will delete your ticket on Ensembl helpdesk.<br>
</div>
<div><br>
</div>
<div>Thanks,</div>
<div>Emily on behalf of the Ensembl Team</div>
<br>
<div class="moz-cite-prefix">On 16/06/2016 11:44, Matiss Ozols
wrote:<br>
</div>
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<p class="MsoNormal">Dear Ensembl team,<o:p></o:p></p>
<p class="MsoNormal">I have a query about mapping from protein
coordinates to genomic coordinates:<o:p></o:p></p>
<p class="MsoNormal">When I map each amino acid I usually expect
to get 3 nucleic acid coordinates, however in some cases I get
only 2 or 1 coordinates. What would be the reason for this?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I use python to do this and my code is
following:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">ext =
"<a class="moz-txt-link-freetext" href="http:/grch37.rest.ensembl.org/map/translation/">http:/grch37.rest.ensembl.org/map/translation/</a><span
style="color:black;mso-fareast-language:EN-GB">ENSP00000325527</span>/82..82;<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">this gives me a result: <span
style="color:black;mso-fareast-language:EN-GB">
[48905207] – why is it just one nucleic acid coordinate
instead of 3?<o:p></o:p></span></p>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB"><o:p> </o:p></span></p>
<p class="MsoNormal"><span
style="color:black;mso-fareast-language:EN-GB">In other case
:
</span>ext = "<a class="moz-txt-link-freetext" href="http:/grch37.rest.ensembl.org/map/translation/">http:/grch37.rest.ensembl.org/map/translation/</a><span
style="color:black;mso-fareast-language:EN-GB">ENSP00000325527</span>/54..54;
Gives me :
<span style="color:black;mso-fareast-language:EN-GB">[48936803|
48936804]<o:p></o:p></span></p>
<p class="MsoNormal">;<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">However most of the time it is 3
coordinates as I expect it to be.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hope you can help,<o:p></o:p></p>
<p class="MsoNormal">Best regards,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">Matiss
Ozols (Beng),<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">PhD
researcher, School of Inflamation & Repair,
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="mso-fareast-language:EN-GB">University
of Manchester<span style="color:#1F497D"><o:p></o:p></span></span></p>
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<br>
<pre class="moz-signature" cols="72">--
Dr Emily Perry (Pritchard)
Ensembl Outreach Project Leader
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge
CB10 1SD
UK </pre>
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