<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:st1="urn:schemas-microsoft-com:office:smarttags" 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 11 (filtered medium)">
<base href="x-msg://463/">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]--><o:SmartTagType
namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PostalCode"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="country-region"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="City"/>
<o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="place"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 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:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:blue;
text-decoration:underline;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@page Section1
{size:612.0pt 792.0pt;
margin:72.0pt 90.0pt 72.0pt 90.0pt;}
div.Section1
{page:Section1;}
-->
</style>
</head>
<body lang=EN-US link=blue vlink=blue style='word-wrap: break-word;-webkit-nbsp-mode: space;
-webkit-line-break: after-white-space'>
<div class=Section1>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thanks a lot Nathan!<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>I will give that a go now.<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Best, <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'><br>
Gavin<o:p></o:p></span></font></p>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>From:</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> Nathan Johnson
[mailto:njohnson@ebi.ac.uk] <br>
<b><span style='font-weight:bold'>Sent:</span></b> 07 December 2010 13:13<br>
<b><span style='font-weight:bold'>To:</span></b> Oliver, Gavin<br>
<b><span style='font-weight:bold'>Cc:</span></b> dev@ensembl.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [SPAM] - Re:
[ensembl-dev] UTR extension for array mapping - Email found in subject</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hi Gavin<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Setting the -utr_multiplier to 0 and omitting any other utr extension
params will just use the transcript model i.e annotated UTRs. The reason why
you are not getting any mappings is unclear to me at the moment as I don't
really know anything about the array model you are mapping, but it maybe
because the ensembl UTR annotations are conservative with repect the the
transcript model which were use to design the probe/set. This is exactly
why we define UTR extension parameters. More details can be found here:<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><a
href="http://www.ensembl.org/info/docs/microarray_probe_set_mapping.html">http://www.ensembl.org/info/docs/microarray_probe_set_mapping.html</a><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>To set the 'Ensembl' defaults automatically you need to set
-calculate_utrs -utr_multiplier 1<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Nath<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On 7 Dec 2010, at 12:43, Oliver, Gavin wrote:<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
<br>
<o:p></o:p></span></font></p>
<div link=blue vlink=purple>
<div>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Hi,<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>They looked straightforward enough but I have managed to
confuse myself with the UTR extensions in the EFG array mapping environment.<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>Basically I only want to map to a UTR if I can actually see
it in the genome browser.<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'> <u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>What settings should I use?<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'>I tried setting all extensions to 0 but this resulted in
zero annotation.<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><font size=2 face=Arial><span style='font-size:10.0pt;
font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='line-height:18.0pt'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Best,<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='line-height:18.0pt'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'><u1:p> </u1:p></span></font><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal style='line-height:18.0pt'><font size=2 face=Arial><span
style='font-size:10.0pt;font-family:Arial'>Gavin</span></font><o:p></o:p></p>
</div>
<u1:p></u1:p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><u1:p> </u1:p><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><strong><b><font size=3 color=blue face="Times New Roman"><span
style='font-size:12.0pt;color:blue'> </span></font></b></strong><o:p></o:p></p>
</div>
<div>
<p class=MsoNormal><b><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;color:black;font-weight:bold'>The contents
of this message and any attachments to it are confidential and may be legally
privileged. If you have received this message in error, you should delete it
from your system immediately and advise the sender.<u1:p></u1:p></span></font><o:p></o:p></b></p>
</div>
<div>
<p class=MsoNormal><b><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;color:black;font-weight:bold'><u1:p> </u1:p></span></font><o:p></o:p></b></p>
</div>
<div>
<p class=MsoNormal><b><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;color:black;font-weight:bold'>Almac Group
(UK) Limited, registered no. NI061368. <span class=apple-converted-space> </span>Almac
Sciences Limited, registered no. NI041550. <span
class=apple-converted-space> </span>Almac Discovery Limited, registered
no. NI046249.<span class=apple-converted-space> </span> Almac Pharma
Services Limited, registered no. NI045055. <span
class=apple-converted-space> </span>Almac Clinical Services Limited,
registered no. NI041905. <span class=apple-converted-space> </span>Almac
Clinical Technologies Limited, registered no. NI061202.<span
class=apple-converted-space> </span> Almac Diagnostics Limited,
registered no. NI043067. <span class=apple-converted-space> </span>All
preceding companies are registered in<span class=apple-converted-space> <st1:country-region u2:st="on"></span><st1:country-region
w:st="on">Northern Ireland</st1:country-region></st1:country-region><span
class=apple-converted-space> </span>with a registered office address of
Almac House, 20 Seagoe Industrial Estate,<span class=apple-converted-space> <st1:place u2:st="on"><st1:city u2:st="on"></span><st1:place
w:st="on"><st1:City w:st="on">Craigavon</st1:city></st1:City>,<span
class=apple-converted-space> <st1:postalcode u2:st="on"></span><st1:PostalCode
w:st="on">BT63 5QD</st1:postalcode></st1:PostalCode>,<span
class=apple-converted-space> <st1:country-region u2:st="on"></span><st1:country-region
w:st="on">UK</st1:country-region></st1:place></st1:country-region></st1:place>.<span
class=apple-converted-space> </span> <u1:p></u1:p></span></font><o:p></o:p></b></p>
</div>
<div>
<p class=MsoNormal><b><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;color:black;font-weight:bold'><u1:p> </u1:p></span></font><o:p></o:p></b></p>
</div>
<div>
<p class=MsoNormal><b><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;color:black;font-weight:bold'>Almac Sciences
(<st1:country-region u2:st="on"><st1:country-region w:st="on">Scotland</st1:country-region></st1:country-region>)
Limited, registered in<span class=apple-converted-space> <st1:country-region u2:st="on"><st1:place u2:st="on"></span><st1:country-region
w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region></st1:place></st1:country-region><span
class=apple-converted-space> </span>no. SC154034.<u1:p></u1:p></span></font><o:p></o:p></b></p>
</div>
<div>
<p class=MsoNormal><b><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;color:black;font-weight:bold'><u1:p> </u1:p></span></font><o:p></o:p></b></p>
</div>
<div>
<p class=MsoNormal><b><font size=3 color=black face="Times New Roman"><span
lang=EN-GB style='font-size:12.0pt;color:black;font-weight:bold'>Almac Clinical
Services LLC, Almac Clinical Technologies LLC, Almac Diagnostics LLC, Almac
Pharma Services LLC and Almac Sciences LLC are Delaware limited liability
companies and Almac Group Incorporated is a Delaware Corporation. More
information on the Almac Group can be found on the Almac website:<span
class=apple-converted-space> </span><a href="http://www.almacgroup.com">www.almacgroup.com</a><u1:p></u1:p></span></font><o:p></o:p></b></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>_______________________________________________<br>
Dev mailing list<br>
<a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>
<a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><o:p></o:p></span></font></p>
</div>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div><span style='orphans: 2;text-align:auto;widows: 2;-webkit-border-horizontal-spacing: 0px;
-webkit-border-vertical-spacing: 0px;-webkit-text-decorations-in-effect: none;
-webkit-text-size-adjust: auto;-webkit-text-stroke-width: 0;word-spacing:0px'><span
style='-webkit-border-horizontal-spacing: 0px;-webkit-border-vertical-spacing: 0px;
-webkit-text-decorations-in-effect: none;-webkit-text-size-adjust: auto;
orphans: 2;widows: 2;word-spacing:0px'>
<div>
<p class=MsoNormal><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'><span
style='-webkit-border-horizontal-spacing: 0px;-webkit-border-vertical-spacing: 0px;
-webkit-text-decorations-in-effect: none;-webkit-text-size-adjust: auto;
orphans: 2;widows: 2;word-spacing:0px'><span style='-webkit-border-horizontal-spacing: 0px;
-webkit-border-vertical-spacing: 0px;-webkit-text-decorations-in-effect: none;
-webkit-text-size-adjust: auto;orphans: 2;widows: 2;word-spacing:0px'>Nathan
Johnson<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'>Scientific Programmer<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'>European
Bioinformatics Institute<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'>Wellcome Trust Genome
Campus<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'>Hinxton<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><st1:City w:st="on"><st1:place w:st="on"><font size=1
color=black face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;
color:black'>Cambridge</span></font></st1:place></st1:City><font size=1
color=black face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;
color:black'> CB10 1SD<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'>Email: <a
href="mailto:njohnson@ebi.ac.uk">njohnson@ebi.ac.uk</a><o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'>TelNo: (+44)1223
492629<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'><o:p> </o:p></span></font></p>
</div>
<p class=MsoNormal><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'><br>
<br>
</span></font><o:p></o:p></p>
</div>
</span></span></span></span>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</div>
<!--[object_id=#almacgroup.com#]--><FONT face=Tahoma size=2>
<P class=MsoNormal><STRONG><B><SPAN style="FONT-SIZE: 12pt; COLOR: blue"><FONT face="Times New Roman"> </FONT></P>
<P class=MsoNormal><FONT color=#000000><SPAN lang=EN-GB style="FONT-FAMILY: 'Times New Roman'">The contents of this message and any attachments to it are confidential and may be legally privileged. If you have received this message in error, you should delete it from your system immediately and advise the sender.<?xml:namespace prefix = o ns = "urn:schemas-microsoft-com:office:office" /><o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="mso-layout-grid-align: none"><FONT color=#0000ff><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Group (UK) Limited, registered no. NI061368.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Sciences Limited, registered no. NI041550.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Discovery Limited, registered no. NI046249. <SPAN style="mso-spacerun: yes"> </SPAN>Almac Pharma Services Limited, registered no. NI045055.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Clinical Services Limited, registered no. NI041905.<SPAN style="mso-spacerun: yes"> </SPAN>Almac Clinical Technologies Limited, registered no. NI061202. <SPAN style="mso-spacerun: yes"> </SPAN>Almac Diagnostics Limited, registered no. NI043067.<SPAN style="mso-spacerun: yes"> </SPAN>All preceding companies are registered in <?xml:namespace prefix = st1 ns = "urn:schemas-microsoft-com:office:smarttags" /><st1:country-region w:st="on">Northern Ireland</st1:country-region> with a registered office address of Almac House, 20 Seagoe Industrial Estate, <st1:place w:st="on"><st1:City w:st="on">Craigavon</st1:City>, <st1:PostalCode w:st="on">BT63 5QD</st1:PostalCode>, <st1:country-region w:st="on">UK</st1:country-region></st1:place>. <SPAN style="mso-spacerun: yes"> </SPAN><o:p></o:p></SPAN></FONT></P>
<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Sciences (<st1:country-region w:st="on">Scotland</st1:country-region>) Limited, registered in <st1:country-region w:st="on"><st1:place w:st="on">Scotland</st1:place></st1:country-region> no. SC154034. <o:p></o:p></SPAN></P>
<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'"><o:p> </o:p></SPAN></P>
<P class=MsoNormal style="mso-layout-grid-align: none"><SPAN lang=EN-GB style="COLOR: black; FONT-FAMILY: 'Times New Roman'">Almac Clinical Services LLC, Almac Clinical Technologies LLC, Almac Diagnostics LLC, Almac Pharma Services LLC and Almac Sciences LLC are Delaware limited liability companies and Almac Group Incorporated is a Delaware Corporation. More information on the Almac Group can be found on the Almac website: <A href="http://www.almacgroup.com">www.almacgroup.com</A><o:p></o:p></SPAN></P></SPAN></B></STRONG></FONT></body>
</html>