<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Gavin<div><br></div><div>To understand what these are, you need to look at them in the database. Look at the unmapped_object table and the unmapped_reason table for more details.</div><div>Either that, or look in the probe2transcript output, as described in the array_mapping.txt documentation.</div><div><br></div><div>Nath</div><div><br></div><div><br></div><div><br></div><div><br><div><div>On 10 Mar 2011, at 13:34, Oliver, Gavin wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><o:smarttagtype namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="place">
<o:smarttagtype namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="City">
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<div class="Section1"><p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:
10.0pt;font-family:Arial;color:navy">Any ideas on this Nathan? With so
many unmapped objects does it suggest some problem with the reference data i.e.
my funcgen database?<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"><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>
<div>
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<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"> Oliver, Gavin <br>
<b><span style="font-weight:bold">Sent:</span></b> 09 March 2011 08:26<br>
<b><span style="font-weight:bold">To:</span></b> 'Nathan Johnson'<br>
<b><span style="font-weight:bold">Cc:</span></b> dev<br>
<b><span style="font-weight:bold">Subject:</span></b> RE: [ensembl-dev] Almost
no annotation with v61 EFG Array Mapping</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="2" color="navy" face="Arial"><span style="font-size:
10.0pt;font-family:Arial;color:navy">Hi 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">Most seem to be unmapped (see the stats
below).<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">Monitor looks fine.<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">Any ideas? Undoubtedly it will be
something simple I’m overlooking!<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"><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">:: Logging
probesets that don't map to any transcripts - Tue Mar 8 17:25:20 2011<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">:: Updating
0 promiscuous probesets - Tue Mar 8 17:38:45 2011<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">::
UnmappedObjects
loaded:
598994<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">::
ADXBRCv2a520413 distinct ProbeSet xrefs mapped(total xrefs):
1/60856(1)<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">::
ADXOCv1a520630 distinct ProbeSet xrefs mapped(total
xrefs): 4/120373(7)<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">::
ADXECv1a520743 distinct ProbeSet xrefs mapped(total
xrefs): 4/111012(7)<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">::
ADXLCv1a520538 distinct ProbeSet xrefs mapped(total
xrefs): 4/60416(10)<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">::
ADXCRCG2a520319 distinct ProbeSet xrefs mapped(total xrefs):
2/61528(2)<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">::
ADXPCv1a520642 distinct ProbeSet xrefs mapped(total
xrefs): 2/121563(2)<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">::
HG-U133_Plus_2 distinct ProbeSet xrefs mapped(total
xrefs): 1/54675(4)<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">:: Mapped
9/167074 transcripts - Tue Mar 8 17:38:57 2011<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>
<div>
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<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> 03 March 2011 11:09<br>
<b><span style="font-weight:bold">To:</span></b> Oliver, Gavin<br>
<b><span style="font-weight:bold">Cc:</span></b> dev<br>
<b><span style="font-weight:bold">Subject:</span></b> Re: [ensembl-dev] Almost
no annotation with v61 EFG Array Mapping</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">Have you checked the unmapped objects? These should give you a clue.<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">Also, you might want to check the pipeline output i.e. 'monitor'
and the ProbeAlign reports. This should show you see exactly what features you
are trying to xref.<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>
<div><p class="MsoNormal"><font size="1" face="Times New Roman"><span style="font-size:
8.0pt">Nathan Johnson<o:p></o:p></span></font></p>
</div>
<div><p class="MsoNormal"><font size="1" face="Times New Roman"><span style="font-size:
8.0pt">Scientific Programmer<o:p></o:p></span></font></p>
</div>
<div><p class="MsoNormal"><font size="1" face="Times New Roman"><span style="font-size:
8.0pt">European Bioinformatics Institute<o:p></o:p></span></font></p>
</div>
<div><p class="MsoNormal"><font size="1" face="Times New Roman"><span style="font-size:
8.0pt">Wellcome Trust Genome Campus<o:p></o:p></span></font></p>
</div>
<div><p class="MsoNormal"><font size="1" face="Times New Roman"><span style="font-size:
8.0pt">Hinxton<o:p></o:p></span></font></p>
</div>
<div><p class="MsoNormal"><st1:place w:st="on"><st1:city w:st="on"><font size="1" face="Times New Roman"><span style="font-size:8.0pt">Cambridge</span></font></st1:city></st1:place><font size="1"><span style="font-size:8.0pt"> CB10 1SD<o:p></o:p></span></font></p>
</div>
<div><p class="MsoNormal"><font size="1" face="Times New Roman"><span style="font-size:
8.0pt">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" face="Times New Roman"><span style="font-size:
8.0pt">TelNo: (+44)1223 492629<o:p></o:p></span></font></p>
</div>
<div><p class="MsoNormal"><font size="1" face="Times New Roman"><span style="font-size:
8.0pt"><o:p> </o:p></span></font></p>
</div>
<div><p class="MsoNormal"><font size="1" face="Times New Roman"><span style="font-size:
8.0pt"><o:p> </o:p></span></font></p>
</div>
</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 2 Mar 2011, at 12:31, Oliver, Gavin wrote:<o:p></o:p></span></font></p>
</div><p class="MsoNormal" style="margin-bottom:12.0pt"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><o:p> </o:p></span></font></p>
<span style="orphans: 2;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: 0px;word-spacing:
0px">
<div link="blue" vlink="purple">
<div><p class="MsoNormal" style="line-height:16.3pt"><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" style="line-height:16.3pt"><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:16.3pt"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">I have rerun my array annotations
with v61. Everything seemed fine until I looked at the log and saw that
perhaps 2 probesets per array have actually mapped to a transcript.<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div><p class="MsoNormal" style="line-height:16.3pt"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">Can you think of something obvious
that might have gone wrong here? The log output is below.<u1:p></u1:p></span></font><o:p></o:p></p>
</div>
<div><p class="MsoNormal" style="line-height:16.3pt"><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:16.3pt"><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:16.3pt"><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:16.3pt"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">Gavin<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"><u1:p> </u1:p></span></font><o:p></o:p></p>
</div>
<div><p class="MsoNormal" style="line-height:16.3pt"><font size="2" face="Arial"><span style="font-size:10.0pt;font-family:Arial">(Nathan I’m posting here
incase you didn’t receive my mail)</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"><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"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">:: ::
Running on<span class="apple-converted-space"> </span><a href="http://probe2transcript.pl/">probe2transcript.pl</a><span class="apple-converted-space"> </span>on:<span class="apple-converted-space"> </span><a href="http://ni-cr-svc-slv.phar-services.com/">ni-cr-svc-slv.phar-services.com</a>
:: :: - Mon Feb 21 09:01:02 2011<u1:p></u1:p><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"><u1:p> </u1:p><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">:: Params are:
--species homo_sapiens --transcript_dbname homo_sapiens_core_61_37f
--transcript_host ni-cr-svc-bs3 --transcript_port 3306 --transcript_user root
--transcript_pass pass --xref_host ni-cr-svc-bs3 --xref_dbname homo_sapiens_funcgen_61_37f
--xref_user root --xref_pass pass --unannotated_5_utr 0 --unannotated_3_utr 0
-annotated_5_prime_extend 0 -annotated_3_prime_extend 0 --threshold 0.000005
--mismatches 2 -vendor AFFY -format AFFY_UTR -arrays ADXOCv1a520630 ADXBRCv2a520413
ADXECv1a520743 ADXLCv1a520538 ADXCRCG2a520319 HG-U133_Plus_2 ADXPCv1a520642
-import_edb<u1:p></u1:p><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">:: No probe DB params specified,
defaulting to xref params<u1:p></u1:p><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"><u1:p> </u1:p><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"><u1:p> </u1:p><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">:: ::
Checking existing Xrefs :: ::<u1:p></u1:p><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"><u1:p> </u1:p><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">:: You have specified -utr_multiplier and
a -3|5_prime_extend, -3|5_prime_extend will override where appropriate<u1:p></u1:p><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 3 unannotated UTR length to 0<u1:p></u1:p><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 5 unannotated UTR length to 0<u1:p></u1:p><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">:: Identified 167074 transcripts for
probe mapping<u1:p></u1:p><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">:: Allowed mismatches = 2<u1:p></u1:p><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">:: Caching arrays per ProbeSet - Mon Feb
21 09:01:21 2011<u1:p></u1:p><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">:: Performing overlap analysis. %
Complete:<u1:p></u1:p><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">:: 0 :: 1
:: 2 :: 3 :: 4
:: 5 :: 6 :: 7
:: 8 :: 9 :: 10
:: 11 :: 12 :: 13 :: 14
:: 15 :: 16 :: 17 :: 18
:: 19 :: 20 :: 21 :: 22
:: 23 :: 24 :: 25 :: 26
:: 27 :: 28 :: 29 :: 30 ::
31 :: 32 :: 33 :: 34 :: 35
:: 36 :: 37 :: 38 :: 39
:: 40 :: 41 :: 42 :: 43
:: 44 :: 45 :: 46 :: 47
:: 48 :: 49 :: 50 :: 51
:: 52 :: 53 :: 54 :: 55
:: 56 :: 57 :: 58 :: 59
:: 60 :: 61 :: 62 :: 63
:: 64 :: 65 :: 66 :: 67
:: 68 :: 69 :: 70 :: 71
:: 72 :: 73 :: 74 :: 75
:: 76 :: 77 :: 78 :: 79
:: 80 :: 81 :: 82 :: 83
:: 84 :: 85 :: 86 :: 87
:: 88 :: 89 :: 90 :: 91
:: 92 :: 93 :: 94 :: 95
:: 96 :: 97 :: 98 :: 99 ::<u1:p></u1:p><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">:: Failed to extend 1 transcripts<u1:p></u1:p><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">:: Seen 0 5 prime UTRs with and average
length of 0<u1:p></u1:p><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">:: Seen 0 3 prime UTRs with and average
length of 0<u1:p></u1:p><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"><u1:p> </u1:p><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"><u1:p> </u1:p><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">:: ::
Writing ADXOCv1a520630 ADXBRCv2a520413 ADXECv1a520743 ADXLCv1a520538
ADXCRCG2a520319 HG-U133_Plus_2 ADXPCv1a520642
Xrefs ::
:: - Mon Feb 21 18:26:37 2011<u1:p></u1:p><o:p></o:p></span></font></p>
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12.0pt"><u1:p> </u1:p><o:p></o:p></span></font></p>
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12.0pt">:: Logging probesets that don't map to
any transcripts - Mon Feb 21 18:26:37 2011<u1:p></u1:p><o:p></o:p></span></font></p>
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12.0pt">:: Updating 0 promiscuous probesets - Mon
Feb 21 18:40:28 2011<u1:p></u1:p><o:p></o:p></span></font></p>
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12.0pt">:: UnmappedObjects
loaded:
598994<u1:p></u1:p><o:p></o:p></span></font></p>
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12.0pt">:: ADXBRCv2a520413 distinct ProbeSet
xrefs mapped(total xrefs): 1/60856(1)<u1:p></u1:p><o:p></o:p></span></font></p>
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12.0pt">:: ADXOCv1a520630 distinct ProbeSet xrefs
mapped(total xrefs): 4/120373(7)<u1:p></u1:p><o:p></o:p></span></font></p>
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12.0pt">:: ADXECv1a520743 distinct ProbeSet xrefs
mapped(total xrefs): 4/111012(7)<u1:p></u1:p><o:p></o:p></span></font></p>
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12.0pt">:: ADXLCv1a520538 distinct ProbeSet xrefs
mapped(total xrefs): 4/60416(10)<u1:p></u1:p><o:p></o:p></span></font></p>
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12.0pt">:: ADXCRCG2a520319 distinct ProbeSet
xrefs mapped(total xrefs): 2/61528(2)<u1:p></u1:p><o:p></o:p></span></font></p>
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<div><p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">:: HG-U133_Plus_2 distinct ProbeSet xrefs
mapped(total xrefs): 1/54675(4)<u1:p></u1:p><o:p></o:p></span></font></p>
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<div><p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">:: ADXPCv1a520642 distinct ProbeSet xrefs
mapped(total xrefs): 2/121563(2)<u1:p></u1:p><o:p></o:p></span></font></p>
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12.0pt">:: Mapped 9/167074 transcripts -
Mon Feb 21 18:40:39 2011<u1:p></u1:p><o:p></o:p></span></font></p>
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12.0pt"><o:p> </o:p></span></font></p>
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<!--[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></span></b></strong></p><strong><b><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.<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 <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></b></strong></font></div>
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<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -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; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><span class="Apple-style-span" style="border-collapse: separate; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; -webkit-text-decorations-in-effect: none; text-indent: 0px; -webkit-text-size-adjust: auto; text-transform: none; orphans: 2; white-space: normal; widows: 2; word-spacing: 0px; "><div>Nathan Johnson</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Scientific Programmer</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">European Bioinformatics Institute</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Wellcome Trust Genome Campus</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Hinxton</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Cambridge CB10 1SD</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Email: <a href="mailto:njohnson@ebi.ac.uk">njohnson@ebi.ac.uk</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">TelNo: (+44)1223 492629</div><div><br class="khtml-block-placeholder"></div><div><br class="khtml-block-placeholder"></div><br class="Apple-interchange-newline"></span></span></span></span><br class="Apple-interchange-newline">
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