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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;">Thank you, i was starting to think i was doing something wrong. I hope it can be fixed soon. Currently i'm using the archive of biomart, but the server seems very unstable and i get many connection problems.</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;">Regards</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</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 Tuesday 22 May 2012 11.38:27 Rhoda Kinsella 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;">Hi Beat</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;">We are currently looking into why this has occurred but it is certainly a bug in our mart databases. I will respond as soon as we have a fix in place. Thank you for reporting this and apologies for any inconvenience.</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;">Regards</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;">Rhoda</p>
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<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;">On 19 May 2012, at 15:55, Beat Wolf wrote:<br /></p>
<p style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; -qt-user-state:0;"><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000;">Hi,</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:'DejaVu Sans'; 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:'DejaVu Sans'; font-size:medium; color:#000000;">i'm a computer scientist and not a biologist, so perhaps i missed something about the DMD gene changing recently.</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:'DejaVu Sans'; font-size:medium; color:#000000;">I have an automated unit test for my application that uses biomart. It happens to test the DMD-001 transcript of the DMD gene.</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:'DejaVu Sans'; font-size:medium; color:#000000;">I</span><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#1f1c1b;">n the 66 version of enembl, the UTR3 coordinates of the exon number 79 where:</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:'DejaVu Sans'; font-size:medium; color:#000000;"> </span></p>
<table border="0" style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px;" cellspacing="2" cellpadding="0">
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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-family:'DejaVu Sans'; 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-family:'DejaVu Sans'; 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=" font-family:'DejaVu Sans'; font-size:medium; color:#1f1c1b;">which was correct. Now with the version 67 of ensembl, the UTR3 region in the same exon is:</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:'DejaVu Sans'; font-size:medium; color:#000000;"> </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-family:'DejaVu Sans'; 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-family:'DejaVu Sans'; 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;"><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000;">Which can not be correct, because that means that UTR3 has a length of 1. The other numbers don't match up either.</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:'DejaVu Sans'; 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:'DejaVu Sans'; font-size:medium; color:#000000;">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.</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:'DejaVu Sans'; 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:'DejaVu Sans'; font-size:medium; color:#000000;">Greetings</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:'DejaVu Sans'; 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:'DejaVu Sans'; font-size:medium; color:#000000;">Beat Wolf</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:'DejaVu Sans'; 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:'DejaVu Sans'; font-size:medium; color:#000000;">On Thursday 10 May 2012 10:58:58 Thomas Maurel wrote:<br /></span></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=" font-family:'DejaVu Sans'; font-size:medium; color:#000000; background-color:#000000;">The latest Ensembl update (e!67) has been released : </span><a href="http://www.ensembl.org/"><span style=" font-family:'DejaVu Sans'; font-size:medium; text-decoration: underline; color:#0057ae; background-color:#000000;">http://www.ensembl.org/</span></a><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000;"><br /><br /></span><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000; background-color:#000000;">Here are some highlights:</span><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000;"><br /><br /></span><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000; background-color:#000000;">Human: The patches for the human genome assembly have been updated to GRCh37.p7, 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;"><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000;"><br />New species: Nile tilapia (Oreochromis niloticus).<br /><br />New genomes: The assemblies for Pig and Squirrel have been updated.</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;"><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000;"><br />A complete list of the changes in release 67 can be found at </span><a href="http://www.ensembl.org/info/website/news.html"><span style=" font-family:'DejaVu Sans'; font-size:medium; text-decoration: underline; color:#0057ae;">http://www.ensembl.org/info/website/news.html</span></a><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000;"><br /><br />For the latest news on the ensembl project visit our blog at </span><a href="http://www.ensembl.info/"><span style=" font-family:'DejaVu Sans'; font-size:medium; text-decoration: underline; color:#0057ae;">http://www.ensembl.info/</span></a><span style=" font-family:'DejaVu Sans'; font-size:medium; 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;"><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000; 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;"><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000;">The release blog post can be viewed here : </span><a href="http://www.ensembl.info/blog/2012/05/10/ensembl-67-has-been-released/"><span style=" font-family:'DejaVu Sans'; font-size:medium; 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;"><span style=" font-family:'DejaVu Sans'; font-size:medium; 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;"><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000; 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=" font-family:'DejaVu Sans'; font-size:medium; color:#000000; 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;"><span style=" font-family:'DejaVu Sans'; font-size:medium; 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;"><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>
<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:'DejaVu Sans'; font-size:medium; 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;"><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000;"><br /><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;"><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000;">_______________________________________________<br />Dev mailing list </span><a href="mailto:Dev@ensembl.org"><span style=" font-family:'DejaVu Sans'; font-size:medium; text-decoration: underline; color:#0057ae;">Dev@ensembl.org</span></a><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000;"><br />List admin (including subscribe/unsubscribe): </span><a href="http://lists.ensembl.org/mailman/listinfo/dev"><span style=" font-family:'DejaVu Sans'; font-size:medium; text-decoration: underline; color:#0057ae;">http://lists.ensembl.org/mailman/listinfo/dev</span></a><span style=" font-family:'DejaVu Sans'; font-size:medium; color:#000000;"><br />Ensembl Blog: </span><a href="http://www.ensembl.info/"><span style=" font-family:'DejaVu Sans'; font-size:medium; text-decoration: underline; color:#0057ae;">http://www.ensembl.info/</span></a><span style=" font-family:'DejaVu Sans'; font-size:medium; 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;"><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;">Rhoda Kinsella Ph.D.</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;">Ensembl Production Project Leader,</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;">European Bioinformatics Institute (EMBL-EBI),<br />Wellcome Trust Genome Campus, </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;">Hinxton<br />Cambridge CB10 1SD,</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;">UK.</span></p>
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