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Hi<br>
<br>
Given a novel variation feature i was wondering how to find out if a
dbSNP record existed for it. In other words, i was wondering if any
known snps were colocated with it. I saw this code in wll mclaren's
snp predictor program<br>
<font face="Courier New"><br>
# find any co-located existing VFs<br>
my $existing_vf = "-";<br>
<br>
if(defined($new_vf->adaptor->db) &&
$check_existing == 1) {<br>
my $fs = $new_vf->feature_Slice;<br>
if($fs->start > $fs->end) {<br>
($fs->{'start'}, $fs->{'end'}) =
($fs->{'end'}, $fs->{'start'});<br>
}<br>
foreach my
$existing_vf_obj(@{$new_vf->adaptor->fetch_all_by_Slice($fs)})
{<br>
$existing_vf = $existing_vf_obj->variation_name<br>
if $existing_vf_obj->seq_region_start ==
$new_vf->seq_region_start<br>
and $existing_vf_obj->seq_region_end ==
$new_vf->seq_region_end;<br>
}<br>
}<br>
</font><br>
<br>
questions:<br>
<br>
1. I believe the feature slice for a feature is defined as the
region exactly spanned by the feature. Does that mean its one bp for
a snp?<br>
<br>
2. Is it possible that the 'matching' dbsnp record could describe
the snp as being on the opposite strand to my snp, or does ensembl
do any internal procesing to make sure all snps are on the forward
strand?<br>
<br>
3. why might the feature slice start be greater than the feature
slice end? I know this script is used for other variations than snps
so it might have something to do with that perhaps?<br>
<br>
4. Can i just confirm the variation_name will give the dbsnp id if
it is a known snp. Could it give anything else? I presume the same
snp can be held in multiple databases used as external references by
ensembl.<br>
<br>
5. I must be reading this code wrong because it doesnt look to me as
if it concatenates a list of dbsnp ids in the variable <font
face="Courier New">$existing_vf</font>, it looks as though it is
overwriting this variable with each snp found<br>
<br>
<br>
thanks a lot<br>
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