<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#FFFFFF" text="#000000">
I recently reviewed the way Ensembl fetches and renders sequence
regions and discovered that labels like 'chromosome' and 'contig'
are fixed, not configurable, and rendered in one particular way as a
track (on pages with tracks displayed). The sequence region track
has the fixed label 'Contigs'. It displays your sequence level
(lowest rank) coordinate system in alternating blue shaded regions
and allows you to navigate by pop-up menu to a region centered on
the contig. <br>
-Jay<br>
<br>
On 06/08/2012 11:39, PATERSON Trevor wrote:
<blockquote
cite="mid:4B2DE8422AF25D40820C088EF2AE5D271F5420D146@EXSEEDMD.is.ed.ac.uk"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=ISO-8859-1">
<meta name="Generator" content="Microsoft Word 14 (filtered
medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
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;}
span.EmailStyle17
{mso-style-type:personal-compose;
font-family:"Calibri","sans-serif";
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-family:"Calibri","sans-serif";
mso-fareast-language:EN-US;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:72.0pt 72.0pt 72.0pt 72.0pt;}
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]-->
<div class="WordSection1">
<p class="MsoNormal">Could someone clarify the significance of
naming a top-level coordinate-system as ‘group’ rather than
‘chromosome’?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">There is one species (stickleback) in
Ensembl that has a top-ranked coordinate system called
‘group’, rather than ‘chromosome’.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">There is a karyotype page for stickleback
and these ‘groups’ are described as chromosomes: there is no
indication of what significance the name ‘group’ has.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I cannot find any other coordinate system
called ‘group’, but in EnsemblGenomes the top ranked
coord-system of Drosophila pseudoobscura is named ‘chr-group’
but these do not seem to treated as chromosomes/karyotypes by
the web interface.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I don’t think there is an enumeration of
allowed coordinate-system names, with definitions - maybe
there could be?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">cheers<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">trevor<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span
style="font-size:12.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB">Trevor
Paterson PhD<br>
</span></b><span
style="font-size:12.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB"><a
moz-do-not-send="true"
href="mailto:trevor.paterson@roslin.ed.ac.uk"><span
style="color:blue">trevor.paterson@roslin.ed.ac.uk</span></a></span><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif";mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span
style="font-size:12.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB">Bioinformatics
<br>
The Roslin Institute<br>
Royal (Dick) School of Veterinary Studies<br>
University of Edinburgh<br>
Easter Bush<br>
Midlothian<br>
EH25 9RG<br>
Scotland UK<br>
<br>
phone +44 (0)131 651 9157<br>
<br>
<a moz-do-not-send="true"
href="http://bioinformatics.roslin.ed.ac.uk/"><span
style="color:blue">http://bioinformatics.roslin.ed.ac.uk/</span></a></span><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif";color:black;mso-fareast-language:EN-GB"><br>
</span><span style="font-size:10.0pt;font-family:"Times
New
Roman","serif";color:navy;mso-fareast-language:EN-GB"><br>
</span><span
style="font-size:12.0pt;font-family:"Arial","sans-serif";color:green;mso-fareast-language:EN-GB">Please
consider the environment before printing this e-mail</span><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif";mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"
style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><i><span
style="font-size:10.0pt;font-family:"Times New
Roman","serif";color:navy;mso-fareast-language:EN-GB">The
University of Edinburgh is a charitable body, registered
in Scotland with registration number SC005336</span></i><span
style="font-size:10.0pt;font-family:"Arial","sans-serif";color:navy;mso-fareast-language:EN-GB"><br>
<b>Disclaimer:This e-mail and any attachments are
confidential and intended solely for the use of the
recipient(s) to whom they are addressed. If you have
received it in error, please destroy all copies and inform
the sender.</b></span><span
style="font-size:12.0pt;font-family:"Times New
Roman","serif";mso-fareast-language:EN-GB"> <o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336.
</pre>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
Dev mailing list <a class="moz-txt-link-abbreviated" href="mailto:Dev@ensembl.org">Dev@ensembl.org</a>
List admin (including subscribe/unsubscribe): <a class="moz-txt-link-freetext" href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a>
Ensembl Blog: <a class="moz-txt-link-freetext" href="http://www.ensembl.info/">http://www.ensembl.info/</a>
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Jay Humphrey Ensembl Genomes Web Developer
EMBL-EBI Tel: +44-(0)1223-492682
Wellcome Trust Genome Campus Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK <a class="moz-txt-link-freetext" href="http://www.ensemblgenomes.org/">http://www.ensemblgenomes.org/</a> </pre>
</body>
</html>