<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class=""><div class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 6 Jun 2017, at 20:12, Bradley Ross <<a href="mailto:1br6@queensu.ca" class="">1br6@queensu.ca</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Hello, </div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class=""></div><div style="margin-top: 0px; margin-bottom: 0px;" class="">I am searching the human GRCh38.p10 through ensembl. For example I search the location of the PTEN gene according to the locations given by the NIH site:<a href="https://ghr.nlm.nih.gov/gene/PTEN#sourcesforpage" class="OWAAutoLink" id="LPlnk294406" previewremoved="true">https://ghr.nlm.nih.gov/gene/PTEN#sourcesforpage</a></div><br class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">According<font size="3" class=""> to that site, the PTEN location is 10:</font><span style="color: rgb(32, 32, 32); font-family: Roboto, 'Helvetica Neue', Helvetica, Arial, sans-serif; font-size: 12pt;" class="">87,863,438-87,971,930</span><span style="color: rgb(32, 32, 32); font-family: Roboto, 'Helvetica Neue', Helvetica, Arial, sans-serif;" class=""><font size="3" class="">. </font></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="color: rgb(32, 32, 32); font-family: Roboto, 'Helvetica Neue', Helvetica, Arial, sans-serif;" class=""><font size="3" class=""><br class=""></font></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><font size="3" class=""><font color="#202020" face="Roboto, Helvetica Neue, Helvetica, Arial, sans-serif" class="">I then entered the above location onto the ensembl GRCh38.p10 browser but changed the first number to </font></font><font color="#202020" face="Roboto, Helvetica Neue, Helvetica, Arial, sans-serif" size="3" class="">87,763,438 to move more </font><font color="#202020" face="Roboto, Helvetica Neue, Helvetica, Arial, sans-serif" class="">upstream</font><font color="#202020" face="Roboto, Helvetica Neue, Helvetica, Arial, sans-serif" size="3" class="">. Within the new region of </font><font size="3" class="">10:</font><span style="font-size: 12pt; color: rgb(32, 32, 32); font-family: Roboto, 'Helvetica Neue', Helvetica, Arial, sans-serif;" class="">87,763,438-87,971,930</span><span style="color: rgb(32, 32, 32); font-family: Roboto, 'Helvetica Neue', Helvetica, Arial, sans-serif;" class=""><font size="3" class="">, the sequence AGGTCA should be found but it is not revealed on the ensembl. </font></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="color: rgb(32, 32, 32); font-family: Roboto, 'Helvetica Neue', Helvetica, Arial, sans-serif;" class=""><font size="3" class=""><br class=""></font></span></div><div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="color: rgb(32, 32, 32); font-family: Roboto, 'Helvetica Neue', Helvetica, Arial, sans-serif;" class=""><font size="3" class="">Brad</font></span></div></div><hr tabindex="-1" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; display: inline-block; width: 1255.375px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""></span><div id="divRplyFwdMsg" dir="ltr" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Dev <<a href="mailto:dev-bounces@ensembl.org" class="">dev-bounces@ensembl.org</a>> on behalf of Ben Moore <<a href="mailto:bmoore@ebi.ac.uk" class="">bmoore@ebi.ac.uk</a>><br class=""><b class="">Sent:</b><span class="Apple-converted-space"> </span>June 6, 2017 10:21:31 AM<br class=""><b class="">To:</b><span class="Apple-converted-space"> </span>Ensembl developers list<br class=""><b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ensembl-dev] Ensemble Search Help</font><div class=""> </div></div><div style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Hi Brad,<div class=""><br class=""></div><div class="">We can definitely try and help you. You can get help through this mailing list, or you can send further information to<span class="Apple-converted-space"> </span><a href="mailto:helpdesk@ensembl.org" class="">helpdesk@ensembl.org</a>, which will create a ticket in our helpdesk system, where a member of the Ensembl team will help you directly. In any case, we’d need to know some more information:</div><div class="">- which species are you searching? which genome assembly are you using in your work?</div><div class="">- do you have an example set of genomic coordinates that you have used?</div><div class="">- what do you see (screenshot)? What do you expect to see?</div><div class=""><br class=""></div><div class="">Best wishes</div><div class=""><br class=""></div><div class="">Ben</div><div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On 6 Jun 2017, at 15:15, Bradley Ross <<a href="mailto:1br6@queensu.ca" class="">1br6@queensu.ca</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div id="divtagdefaultwrapper" dir="ltr" class="" style="font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; font-size: 12pt; font-family: Calibri, Arial, Helvetica, sans-serif;"><div class=""><font face="Calibri,Arial,Helvetica,sans-serif,serif,EmojiFont" class="">Hello,</font></div><div class=""><font face="Calibri,Arial,Helvetica,sans-serif,serif,EmojiFont" class=""><br class=""></font></div><div class=""><font face="Calibri,Arial,Helvetica,sans-serif,serif,EmojiFont" class="">I was wondering if there was someone I could contact regarding using the genome browser Ensembl. </font></div><div class=""><font face="Calibri,Arial,Helvetica,sans-serif,serif,EmojiFont" class=""><br class=""></font></div><div class=""><font face="Calibri,Arial,Helvetica,sans-serif,serif,EmojiFont" class="">I have searched specific regions where I know a particular sequence should be located, but it does not come up when I search through this genome browser. </font></div><div class=""><font face="Calibri,Arial,Helvetica,sans-serif,serif,EmojiFont" class=""><br class=""></font></div><div class=""><font face="Calibri,Arial,Helvetica,sans-serif,serif,EmojiFont" class="">Any assistance would be greatly appreciated. </font></div><div class=""><br class=""></div><div class=""><font face="Calibri,Arial,Helvetica,sans-serif,serif,EmojiFont" class="">Brad</font></div></div><span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;">_______________________________________________</span><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;">Dev mailing list </span><a href="mailto:Dev@ensembl.org" class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">Dev@ensembl.org</a><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;">Posting guidelines and subscribe/unsubscribe info:<span class="Apple-converted-space"> </span></span><a href="http://lists.ensembl.org/mailman/listinfo/dev" class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">http://lists.ensembl.org/mailman/listinfo/dev</a><br class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;"><span class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;">Ensembl Blog:<span class="Apple-converted-space"> </span></span><a href="http://www.ensembl.info/" class="" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">http://www.ensembl.info/</a></div></blockquote></div><br class=""><div apple-content-edited="true" class=""><div class="" style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class="" style="letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;"><div class="">Ben Moore</div><div class="">Ensembl Outreach Officer</div><div class=""><br class=""></div><div class="">European Bioinformatics Institute (EMBL-EBI)</div><div class="">European Molecular Biology Laboratory</div><div class="">Wellcome Trust Genome Campus</div><div class="">Hinxton</div><div class="">Cambridge</div><div class="">CB10 1SD</div><div class="">UK</div><div class=""><br class=""></div><div class=""><a href="mailto:bmoore@ebi.ac.uk" class="">bmoore@ebi.ac.uk</a></div><div class="">+44 (0)1223 494265</div></div></div></div><br class=""></div></div><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Dev mailing list <a href="mailto:Dev@ensembl.org" class="">Dev@ensembl.org</a></span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" class="">http://lists.ensembl.org/mailman/listinfo/dev</a></span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Ensembl Blog: <a href="http://www.ensembl.info/" class="">http://www.ensembl.info/</a></span></div></blockquote></div><br class=""><div apple-content-edited="true" class="">
<div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div style="color: rgb(0, 0, 0); letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><div class="">Ben Moore</div><div class="">Ensembl Outreach Officer</div><div class=""><br class=""></div><div class="">European Bioinformatics Institute (EMBL-EBI)</div><div class="">European Molecular Biology Laboratory</div><div class="">Wellcome Trust Genome Campus</div><div class="">Hinxton</div><div class="">Cambridge</div><div class="">CB10 1SD</div><div class="">UK</div><div class=""><br class=""></div><div class=""><a href="mailto:bmoore@ebi.ac.uk" class="">bmoore@ebi.ac.uk</a></div><div class="">+44 (0)1223 494265</div></div></div>
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