<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<meta name="Generator" content="Microsoft Word 14 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:purple;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0in;
mso-margin-bottom-alt:auto;
margin-left:0in;
font-size:12.0pt;
font-family:"Times New Roman","serif";}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:"Calibri","sans-serif";
color:#1F497D;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";}
@page WordSection1
{size:8.5in 11.0in;
margin:1.0in 1.0in 1.0in 1.0in;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="blue" vlink="purple">
<div class="WordSection1">
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks that was helpful<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> dev-bounces@ensembl.org [mailto:dev-bounces@ensembl.org]
<b>On Behalf Of </b>Bert Overduin<br>
<b>Sent:</b> Wednesday, March 06, 2013 10:21 AM<br>
<b>To:</b> Ensembl developers list<br>
<b>Subject:</b> Re: [ensembl-dev] NCBI vs Ensemble<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">Hello Sunita,<br>
<br>
NCBI and Ensembl generate their gene models in different ways, so they can differ in their coordinates, as is the case for the human DNMT3A gene.<br>
<br>
The patches have nothing to do with this as this gene is not located in a patch region.<br>
<br>
Just for your information, we indeed annotate at the moment the GRCh37.p10 assembly. The patches themselves however are existing as separate entities from the reference genome assembly. The reference genome itself has not changed between GRCh37 and GRCh37.p10.
There are basically two kind of patches, novel patches, which represent alternate loci and fix patches, which represent corrected regions. The fix patches will be incorporated in the reference genome assembly in the next major release (i.e. GRCh38), thus replacing
the faulty regions. Until that time genes located in fix patch regions will be annotated both on the reference genome assembly and the fix patch, as you can see for e.g. the human ABO gene:<br>
<br>
<a href="http://www.ensembl.org/Homo_sapiens/Search/Details?db=core;end=2;idx=Gene;q=ABO;species=Homo_sapiens" target="_blank">http://www.ensembl.org/Homo_sapiens/Search/Details?db=core;end=2;idx=Gene;q=ABO;species=Homo_sapiens</a><br>
<br>
But again, this does not pertain to the DNMT3A gene, as it is not located in a fix patch region.<br>
<br>
Hope this helps.<br>
<br>
Cheers,<br>
Bert<o:p></o:p></p>
<div>
<p class="MsoNormal">On Wed, Mar 6, 2013 at 4:03 PM, Koul, Sunita <<a href="mailto:sunita@pathology.wustl.edu" target="_blank">sunita@pathology.wustl.edu</a>> wrote:<o:p></o:p></p>
<div>
<div>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I was looking at the Gene DNMT3A (<span style="font-size:10.0pt;font-family:"Courier New";color:red">ENSG00000119772)
</span> in the ensemble genome browser<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">As per the release the ensemble 70 has updated patches for the human assembly (GRCh37.p10)
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">In NCBI the genomic location of this gene is (25455830-25565459)
<a href="http://www.ncbi.nlm.nih.gov/gene?db=gene&cmd=retrieve&dopt=full_report&list_uids=1788" target="_blank">
http://www.ncbi.nlm.nih.gov/gene?db=gene&cmd=retrieve&dopt=full_report&list_uids=1788</a><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">How is that the ensemble still shows the (25455845-25565459) in their browser
<a href="http://useast.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000119772;r=2:25455845-25565459" target="_blank">
http://useast.ensembl.org/Homo_sapiens/Location/View?db=core;g=ENSG00000119772;r=2:25455845-25565459</a><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b>Am I missing something here?</b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Basically we are trying to annotate our genes with annotations from Ensemble. We are currently using NCBI build 37.p10 and want to pull in more information from Ensemble<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Unless we find the compatibility between these 2 builds we can’t proceed<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Can someone guide me how we can do this<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Sunita<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
<table class="MsoNormalTable" border="0" cellspacing="3" cellpadding="0">
<tbody>
<tr>
<td style="border:none;border-top:solid black 1.0pt;padding:5.25pt .75pt .75pt .75pt">
<p class="MsoNormal"><b><i><span style="font-size:8.5pt;font-family:"Arial","sans-serif"">The materials in this email are private and may contain Protected Health Information. If you are not the intended recipient, be advised that any unauthorized use, disclosure,
copying, distribution or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return email.<o:p></o:p></span></i></b></p>
</td>
</tr>
</tbody>
</table>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev" target="_blank">
http://lists.ensembl.org/mailman/listinfo/dev</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info/</a><o:p></o:p></p>
</div>
<p class="MsoNormal"><br>
<br clear="all">
<br>
-- <br>
Bert Overduin, Ph.D.<br>
Vertebrate Genomics Team<br>
<br>
EMBL - European Bioinformatics Institute<br>
Wellcome Trust Genome Campus<br>
Hinxton, Cambridge CB10 1SD<br>
United Kingdom<br>
<br>
<a href="http://www.ebi.ac.uk/~bert" target="_blank">http://www.ebi.ac.uk/~bert</a><o:p></o:p></p>
<div>
<p style="mso-margin-top-alt:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
<span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Ensembl browser: <a href="http://www.ensembl.org/" target="_blank">http://www.ensembl.org</a></span><o:p></o:p></p>
<p style="mso-margin-top-alt:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
<span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Mailing lists: <span style="color:blue"><a href="http://www.ensembl.org/info/about/contact/mailing.html" target="_blank">http://www.ensembl.org/info/about/contact/mailing.html</a></span></span><span style="font-family:"Arial","sans-serif""><o:p></o:p></span></p>
<p style="mso-margin-top-alt:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
<span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Blog: <span style="color:blue"><a href="http://www.ensembl.info/" target="_blank">http://www.ensembl.info</a></span></span><span style="font-family:"Arial","sans-serif""><o:p></o:p></span></p>
<p style="mso-margin-top-alt:.1pt;margin-right:0in;margin-bottom:0in;margin-left:0in;margin-bottom:.0001pt">
<span style="font-size:10.0pt;font-family:"Arial","sans-serif"">YouTube: <span style="color:#000099"><a href="http://www.youtube.com/user/EnsemblHelpdesk" target="_blank">http://www.youtube.com/user/EnsemblHelpdesk</a></span><br>
Facebook: <span style="color:blue"><a href="http://www.facebook.com/Ensembl.org" target="_blank">http://www.facebook.com/Ensembl.org</a></span><br>
Twitter: <span style="color:blue"><a href="http://twitter.com/Ensembl" target="_blank">http://twitter.com/Ensembl</a> </span></span><span style="font-family:"Arial","sans-serif""><o:p></o:p></span></p>
</div>
</div>
</body>
</html>