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<p>Will the fixed biomart also include the missing polyphen_score and sift_score? that would be awesome :)</p>
<p>Beat Wolf</p>
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<td>----- Message d'origine -----</td>
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<td><strong>De:</strong> Rhoda Kinsella <rhoda@ebi.ac.uk></td>
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<td><strong>Date:</strong> Thu, 24 May 2012 09:00:18 +0100</td>
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<td><strong>Sujet:</strong> Re: [ensembl-dev] Biomart Genomic Coding Start/End</td>
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<td><strong>À:</strong> Ensembl developers list <dev@ensembl.org></td>
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Hi Simon
<div>Yes this is likely to be related to the issue below. Can you send me a specific example so that I can check that this? We have rerun the calculations and are in the process of testing to make sure all id okay before copying the fixed mart to the live site. I will send an email once the fix has been made live.</div>
<div>Regards</div>
<div>Rhoda</div>
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<div>On 23 May 2012, at 18:06, Simon Chan wrote:</div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;">Hello,</span></div>
<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;"> </span></div>
<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;">I'm using BioMart to fetch all protein coding portions of all exons of all transcripts of my favourite gene (Ensembl Genes 67, Homo sapiens genes GRCh37.p7). In the past, 'Genomic coding start' and 'Genomic coding end' would give me all exon coordinates minus UTRs. However, now it seems to return the UTR coordinates as well. Perhaps this is related to the UTR issue reported by Beat below?</span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;">Thank you.</span></div>
<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 11pt; font-family: Calibri, sans-serif;">Simon.</span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><strong><span style="font-size: 10pt; font-family: Tahoma, sans-serif;">From:</span></strong><span style="font-size: 10pt; font-family: Tahoma, sans-serif;"><span> </span><a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a> [<a style="color: blue; text-decoration: underline;" href="mailto:dev-bounces@ensembl.org">mailto:dev-bounces@ensembl.org</a>]<span> </span><strong>On Behalf Of<span> </span></strong>Rhoda Kinsella<br /><strong>Sent:</strong><span> </span>Tuesday, May 22, 2012 3:38 AM<br /><strong>To:</strong><span> </span>Ensembl developers list<br /><strong>Subject:</strong><span> </span>Re: [ensembl-dev] Ensembl release 67 is out!</span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"> </div>
<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;">Hi Beat</div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;">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.</div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;">Regards</div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;">Rhoda</div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;">On 19 May 2012, at 15:55, Beat Wolf wrote:</div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;">Hi,</span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; white-space: pre-wrap;"><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;"> </span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;">i'm a computer scientist and not a biologist, so perhaps i missed something about the DMD gene changing recently.</span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;">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></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;">I</span><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: #1f1c1b;">n the 66 version of enembl, the UTR3 coordinates of the exon number 79 where:</span><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;"></span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; white-space: pre-wrap;"><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;"> </span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 13.5pt; color: #1f1c1b;">31137345</span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 13.5pt; color: #1f1c1b;">to 31140035</span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: #1f1c1b;">which was correct. Now with the version 67 of ensembl, the UTR3 region in the same exon is:</span><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;"></span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; white-space: pre-wrap;"><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;"> </span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 13.5pt; color: #1f1c1b;">31137345 to</span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 13.5pt; color: #1f1c1b;">31137344</span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;">Which can not be correct, because that means that UTR3 has a length of 1. The other numbers don't match up either.</span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt; white-space: pre-wrap;"><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;"> </span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;">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></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;">Greetings</span></div>
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<div style="margin-right: 0in; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman', serif; margin-top: 0in; margin-bottom: 0.0001pt;"><span style="font-size: 9pt; font-family: 'DejaVu Sans', serif; color: black;">Beat Wolf</span></div>
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<div>Rhoda Kinsella Ph.D.</div>
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<div style="font: normal normal normal 12px/normal Helvetica; margin: 0px;">Ensembl Production Project Leader,</div>
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<div>European Bioinformatics Institute (EMBL-EBI),<br />Wellcome Trust Genome Campus, </div>
<div>Hinxton<br />Cambridge CB10 1SD,</div>
<div>UK.</div>
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