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<p>Hello Ben,</p>
<p><br>
</p>
<p>My apologies the sequence is supposed to be AGGTCANAGGTCA. I forgot to repeat it in the last email. </p>
<p><br>
</p>
<p>For example, I know the above sequence should be located in the adipocyte fatty-acid binding protein 2 (AP2). Could you conduct the same search (keeping in mind to move the start location back at least 20kb) and tell me whether or not you find the sequence
through ensemble?</p>
<p><br>
</p>
<p>Brad </p>
</div>
<hr style="display:inline-block;width:98%" tabindex="-1">
<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Dev <dev-bounces@ensembl.org> on behalf of Ben Moore <bmoore@ebi.ac.uk><br>
<b>Sent:</b> June 7, 2017 5:16:47 AM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] Ensemble Search Help</font>
<div> </div>
</div>
<div>
<div class="" style="word-wrap:break-word">Hi Brad,
<div class=""><br class="">
</div>
<div class="">I’m not sure exactly what you mean by the sequence not being revealed. However, when I search this genomic region in Ensembl I arrive at the following 'Region in Detail’ page:</div>
<div class=""><a href="http://www.ensembl.org/Homo_sapiens/Location/View?r=10:87763438-87971930;db=core" class="">http://www.ensembl.org/Homo_sapiens/Location/View?r=10:87763438-87971930;db=core</a></div>
<div class=""><br class="">
</div>
<div class="">Once on this page, you can click on the blue ‘Export data’ button on the left hand side of the page, which opens a pop up window where you can select the type of data you want to download from this genomic region. By default, you will download
the FASTA sequence. If you select the default parameters and download the FASTA sequence (which I have done, attached), you will be able to search this genomic sequence for your sequence of interest. I have found that ‘AGGTCA’ occurs multiple times in this
sequence.</div>
<div class=""><br class="">
</div>
<div class="">As a side note, you are able to search directly in Ensembl for the PTEN gene (<a href="http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000171862;r=10:87863113-87971930" class="">http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000171862;r=10:87863113-87971930</a>)
and navigate to the ‘Region in Detail’ page (<a href="http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000171862;r=10:87863113-87971930" class="">http://www.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000171862;r=10:87863113-87971930</a>),
if that helps you find the relevant genomic region(s) for you study.</div>
<div class=""><br class="">
</div>
<div class="">I hope these directions help you find the data you need, but please do get back in touch if you have any further questions.</div>
<div class="">
<div class=""><br class="">
</div>
<div class="">Best wishes</div>
<div class=""><br class="">
</div>
<div class="">Ben</div>
<div class=""><br class="">
</div>
<div class=""></div>
</div>
</div>
<div class="" style="word-wrap:break-word">
<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="x_Apple-interchange-newline">
<div class="">
<div id="x_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; font-size:12pt; font-family:Calibri,Arial,Helvetica,sans-serif">
<div class="" style="margin-top:0px; margin-bottom:0px">Hello, </div>
<div class="" style="margin-top:0px; margin-bottom:0px"><br class="">
</div>
<div class="" style="margin-top:0px; margin-bottom:0px">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="x_OWAAutoLink" id="LPlnk294406">https://ghr.nlm.nih.gov/gene/PTEN#sourcesforpage</a></div>
<br class="">
<div class="" style="margin-top:0px; margin-bottom:0px">According<font size="3" class=""> to that site, the PTEN location is 10:</font><span class="" style="color:rgb(32,32,32); font-family:Roboto,'Helvetica Neue',Helvetica,Arial,sans-serif; font-size:12pt">87,863,438-87,971,930</span><span class="" style="color:rgb(32,32,32); font-family:Roboto,'Helvetica Neue',Helvetica,Arial,sans-serif"><font size="3" class="">. </font></span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="color:rgb(32,32,32); font-family:Roboto,'Helvetica Neue',Helvetica,Arial,sans-serif"><font size="3" class=""><br class="">
</font></span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><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 class="" style="font-size:12pt; color:rgb(32,32,32); font-family:Roboto,'Helvetica Neue',Helvetica,Arial,sans-serif">87,763,438-87,971,930</span><span class="" style="color:rgb(32,32,32); font-family:Roboto,'Helvetica Neue',Helvetica,Arial,sans-serif"><font size="3" class="">,
the sequence AGGTCA should be found but it is not revealed on the ensembl. </font></span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="color:rgb(32,32,32); font-family:Roboto,'Helvetica Neue',Helvetica,Arial,sans-serif"><font size="3" class=""><br class="">
</font></span></div>
<div class="" style="margin-top:0px; margin-bottom:0px"><span class="" style="color:rgb(32,32,32); font-family:Roboto,'Helvetica Neue',Helvetica,Arial,sans-serif"><font size="3" class="">Brad</font></span></div>
</div>
<hr tabindex="-1" 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; display:inline-block; width:1255.375px">
<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; float:none; display:inline!important"></span>
<div id="x_divRplyFwdMsg" dir="ltr" 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">
<font face="Calibri, sans-serif" class="" style="font-size:11pt"><b class="">From:</b><span class="x_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="x_Apple-converted-space"> </span>June 6, 2017 10:21:31 AM<br class="">
<b class="">To:</b><span class="x_Apple-converted-space"> </span>Ensembl developers list<br class="">
<b class="">Subject:</b><span class="x_Apple-converted-space"> </span>Re: [ensembl-dev] Ensemble Search Help</font>
<div class=""> </div>
</div>
<div 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">
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="x_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="x_Apple-interchange-newline">
<div class="">
<div id="x_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; 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>
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<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>
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<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; 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">
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<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>
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