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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;">Hi,</p>
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;">i'm a computer scientist and not a biologist, so perhaps i missed something about the DMD gene changing recently.</p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;">I have an automated unit test for my application that uses biomart. It happens to test the DMD-001 transcript of the DMD gene.</p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;">I<span style=" color:#1f1c1b;">n the 66 version of enembl, the UTR3 coordinates of the exon number 79 where:</span></p>
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><span style=" font-size:medium; color:#1f1c1b;">31137345</span></p></td>
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><span style=" font-size:medium; color:#1f1c1b;">to 31140035</span></p></td></tr></table>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><span style=" color:#1f1c1b;">which was correct. Now with the version 67 of ensembl, the UTR3 region in the same exon is:</span></p>
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><span style=" font-size:medium; color:#1f1c1b;">31137345 to</span></p></td>
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><span style=" font-size:medium; color:#1f1c1b;">31137344</span></p></td></tr></table>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;">Which can not be correct, because that means that UTR3 has a length of 1. The other numbers don't match up either.</p>
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;">Did the DMD gene change? Is the information stored differently in ensembl? What values do i need to reconstruct the true UTR3 region? Or is this a bug in the new ensembl version. If yes, how many other genes are affected? Currently i will stay on the 66 version thanks to the archives, but i have some connection issues with it, it seems to be much less stable than the 67 version.</p>
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;">Greetings</p>
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;">Beat Wolf</p>
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<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;">On Thursday 10 May 2012 10:58:58 Thomas Maurel wrote:<br /></p>
<p style=" margin-top:12px; margin-bottom:12px; margin-left:40px; margin-right:40px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><span style=" background-color:#000000;">The latest Ensembl update (e!67) has been released : </span><a href="http://www.ensembl.org/"><span style=" text-decoration: underline; color:#0057ae; background-color:#000000;">http://www.ensembl.org/</span></a><br /><br /><span style=" background-color:#000000;">Here are some highlights:</span><br /><br /><span style=" background-color:#000000;">Human: The patches for the human genome assembly have been updated to GRCh37.p7, </span><span style=" background-color:#000000;">Human somatic variants from COSMIC have been updated to release 58 and we now provide the 1000 genomes phase 1 genotype data.</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:40px; margin-right:40px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><br />New species: Nile tilapia (Oreochromis niloticus).<br /><br />New genomes: The assemblies for Pig and Squirrel have been updated.</p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:40px; margin-right:40px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><br />A complete list of the changes in release 67 can be found at <a href="http://www.ensembl.org/info/website/news.html"><span style=" text-decoration: underline; color:#0057ae;">http://www.ensembl.org/info/website/news.html</span></a><br /><br />For the latest news on the ensembl project visit our blog at <a href="http://www.ensembl.info/"><span style=" text-decoration: underline; color:#0057ae;">http://www.ensembl.info/</span></a><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><span style=" background-color:#000000;"><br /></span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;">The release blog post can be viewed here : <a href="http://www.ensembl.info/blog/2012/05/10/ensembl-67-has-been-released/"><span style=" text-decoration: underline; color:#0057ae;">http://www.ensembl.info/blog/2012/05/10/ensembl-67-has-been-released/</span></a></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><span style=" background-color:#000000;">Best regards,</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><span style=" background-color:#000000;">Thomas Maurel</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><br /></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><span style=" font-family:'Helvetica'; font-size:medium; color:#000000;">--</span></p>
<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><span style=" font-family:'Helvetica'; font-size:medium; color:#000000;">Thomas Maurel<br />Bioinformatician - Ensembl Production Team<br />European Bioinformatics Institute (EMBL-EBI)<br />Wellcome Trust Genome Campus, Hinxton<br />Cambridge - CB10 1SD - UK</span></p>
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