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Hi Andrea,<br>
<br>
Adding to Fiona's answer, the dbSNP 132 release for cow was slightly
delayed so we were unable to import it in time for the January
Ensembl release (61). This will instead happen for release 62. <br>
<br>
If a variation has no mapping to the genome, you won't get any
variation features at all.<br>
<br>
/Pontus<br>
<br>
<br>
On 09/12/2010 14:27, Andrea Edwards wrote:
<blockquote cite="mid:4D00E73A.6090204@cs.man.ac.uk" type="cite">
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<p><font face="Arial">Dear all</font></p>
<p><br>
<font face="Arial">I was hoping you might be able to help me
with something to do with the incorporation of dbSNP 132 into
ensembl</font></p>
<p><font face="Arial">I was looking at rs43469576 a few weeks ago
in dbSNP and I am 99% positive it said on the webpage in big
red letters that this snp mapped to 3 genome locations. I
checked what ensembl does about this and i have code showing
how ensembl too maps it to 3 genome locations<span
class="Apple-style-span" style="border-collapse: separate;
color: rgb(0, 0, 0); font-family: 'Times New Roman';
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: 2; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
font-size: medium;"><span class="Apple-style-span"
style="font-family: Verdana,arial,sans-serif; font-size:
11px; line-height: 17px; text-align: left;">
<ul style="margin: 16px 0px; padding: 0px 3em; font-size:
11px; line-height: 13pt; list-style-type: disc;">
<li style="font-size: 11px; line-height: 13pt; margin:
0px; padding: 0px;">chr7(65859978), chr7(91674598),
chr6(86134792)</li>
</ul>
Now when i look at dbSNP it says this variation isn't
mapped to any assembly. </span></span></font><font
face="Arial"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
font-family: 'Times New Roman'; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: 2; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family:
Verdana,arial,sans-serif; font-size: 11px; line-height:
17px; text-align: left;">If i search dbsnp for one of
those genome locations (e.g. </span></span><span
class="Apple-style-span" style="border-collapse: separate;
color: rgb(0, 0, 0); font-family: 'Times New Roman';
font-style: normal; font-variant: normal; font-weight:
normal; letter-spacing: normal; line-height: normal;
orphans: 2; text-indent: 0px; text-transform: none;
white-space: normal; widows: 2; word-spacing: 0px;
font-size: medium;"><span class="Apple-style-span"
style="font-family: Verdana,arial,sans-serif; font-size:
11px; line-height: 17px; text-align: left;">chr7(65859978))
rs43469576 </span></span>is no longer in the results</font></p>
<p><font face="Arial"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
font-family: 'Times New Roman'; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: 2; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family:
Verdana,arial,sans-serif; font-size: 11px; line-height:
17px; text-align: left;"></span></span></font></p>
<p><font face="Arial"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
font-family: 'Times New Roman'; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: 2; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family:
Verdana,arial,sans-serif; font-size: 11px; line-height:
17px; text-align: left;">Now i appreciate that I am a
fallible human being and could have got confused but it
looks to me as if dbSNP has changed and now doesn't seem
to show snps as mapping to multiple locations. </span></span>I
looked on their build release notes and schema revisions etc
but there is no mention of this. So perhaps i am mistaken. It
often happens :)</font></p>
<p><font face="Arial"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
font-family: 'Times New Roman'; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: 2; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family:
Verdana,arial,sans-serif; font-size: 11px; line-height:
17px; text-align: left;"></span></span></font></p>
<p><font face="Arial"><span class="Apple-style-span"
style="border-collapse: separate; color: rgb(0, 0, 0);
font-family: 'Times New Roman'; font-style: normal;
font-variant: normal; font-weight: normal; letter-spacing:
normal; line-height: normal; orphans: 2; text-indent: 0px;
text-transform: none; white-space: normal; widows: 2;
word-spacing: 0px; font-size: medium;"><span
class="Apple-style-span" style="font-family:
Verdana,arial,sans-serif; font-size: 11px; line-height:
17px; text-align: left;">But regardless of whether i am
mistaken or not there still exists a difference between
the info in ensembl and dbsnp and I would like to know
what to expect from ensembl in the january release. Will i
still see a variation like </span></span>rs43469576
mapped to multiple genome locations or will it be mapped to no
assembly.<br>
</font></p>
<p><font face="Arial">Which then leads to the next question, what
will you get for a variation feature start/end/chromosome if
it isn't mapped. As i said at present ensembl seems to map the
rs entries in dbSNP that are unmapped so I've not come across
it.<br>
</font></p>
<p><font face="Arial">thanks a lot<br>
</font></p>
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