<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><base href="x-msg://234/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Reece,<div>Just to add to RIshi's answer; only the sequences from RefSeq which align the genome of interest are stored in the otherfeatures database</div><div><br></div><div>Thanks</div><div>Thibaut</div><div><br><div><div>On 4 Jun 2013, at 14:26, Rishi Nag <<a href="mailto:rn6@sanger.ac.uk">rn6@sanger.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="font-family: 'DejaVu Sans Mono'; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">On Tue, 04 Jun 2013 02:22:29 +0100, Reece Hart <<a href="mailto:reece@harts.net">reece@harts.net</a>> wrote:<br><br><blockquote style="margin: 0px 0px 0.8ex; border-left-color: rgb(0, 0, 255); border-left-width: 2px; border-left-style: solid; padding-left: 1ex; "><div dir="ltr">What's the source of the refseq data in otherfeatures? <div><br></div><div>How current is the otherfeatures data?</div></div></blockquote><div><br></div><div>The date of the last release is stored in the otherfeatures meta table with meta_key genebuild.last_otherfeatures_update </div><div><br></div><div>Typically the db_version in the analysis table should record the refseq version being used for the data. However, this may not have been captured for older releases. Data are downloaded from the NCBI website.<br></div><div><br></div><blockquote style="margin: 0px 0px 0.8ex; border-left-color: rgb(0, 0, 255); border-left-width: 2px; border-left-style: solid; padding-left: 1ex; "><div dir="ltr"><div>What reconciliation is done when there are substitutions (e.g., VHL, TNFRSF10C, SERPINE2) or indels (NEFL, ABO, ZAN) in the transcript relative to GRCh37?</div><div><br></div><div>Thanks,</div><div>Reece</div><div><br></div></div></blockquote><br><br><br><div id="M2Signature"><div>--</div><div>Rishi Nag<br>Ensembl Genebuilder<br>Wellcome Trust Sanger Institute<br><a href="http://ensembl.org">http://ensembl.org</a><br><br>Using Opera's mail client:<span class="Apple-converted-space"> </span><a href="http://www.opera.com/mail/">http://www.opera.com/mail/</a></div></div>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info:<span class="Apple-converted-space"> </span><a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog:<span class="Apple-converted-space"> </span><a href="http://www.ensembl.info/">http://www.ensembl.info/</a></div></blockquote></div><br></div></body></html>