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<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Thanks again Will!<o:p></o:p></span></font></p>
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10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
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<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'> wmclaren@gmail.com
[mailto:wmclaren@gmail.com] <b><span style='font-weight:bold'>On Behalf Of </span></b>Will
McLaren<br>
<b><span style='font-weight:bold'>Sent:</span></b> 02 February 2011 16:32<br>
<b><span style='font-weight:bold'>To:</span></b> <st1:PersonName w:st="on">Oliver,
Gavin</st1:PersonName><br>
<b><span style='font-weight:bold'>Cc:</span></b> Graham Ritchie;
dev@ensembl.org<br>
<b><span style='font-weight:bold'>Subject:</span></b> [SPAM] - Re: [SPAM] - Re:
[SPAM] - Re: [SPAM] - Re: [ensembl-dev] Transcript variation alleles - Email
found in subject - Email found in subject - Email found in subject - Email
found in subject</span></font><o:p></o:p></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>A variation is defined by its alleles and a pair of flanking sequence,
e.g.:<o:p></o:p></span></font></p>
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12.0pt'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>ATCGTACTGTACGTGTTTATCG [A/G] TGACTTACTATCGTATGACTT<o:p></o:p></span></font></p>
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12.0pt'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>dbSNP (or in some cases Ensembl) use sequence alignment algorithms to
map this sequence to the genomic reference sequence. If it maps to the reverse
strand, we create a variation_feature on the reverse strand. In some cases the
sequence may map more than once, hence a variation object can have multiple
associated variation_feature objects. This is easier to see on the web views:<o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><a
href="http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=rs78197743;vdb=variation">http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=rs78197743;vdb=variation</a><o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>As I mentioned, it makes our lives easier if most things are on the
forward strand, so we "flip" as many of these reverse strand mappings
as we can. We only do this when a variation has a single mapping to the reverse
strand.<o:p></o:p></span></font></p>
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<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Will<o:p></o:p></span></font></p>
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<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On 2 February 2011 16:17, <st1:PersonName w:st="on">Oliver, Gavin</st1:PersonName>
<<a href="mailto:gavin.oliver@almacgroup.com">gavin.oliver@almacgroup.com</a>>
wrote:<o:p></o:p></span></font></p>
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<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>Cool, thanks.</span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><o:p></o:p></p>
<p class=MsoNormal style='mso-margin-top-alt:auto;mso-margin-bottom-alt:auto'><font
size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'>What determines the strand it goes on?</span></font><o:p></o:p></p>
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size=2 color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
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