<div dir="ltr">Sorry, here's a link to the module documentation:<div><br></div><div><a href="http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1MotifFeatureVariationAllele.html#ac830653283dfdb6b85305373cc6a4d98">http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1MotifFeatureVariationAllele.html#ac830653283dfdb6b85305373cc6a4d98</a><br>
</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 25 February 2014 14:35, Will McLaren <span dir="ltr"><<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hello Mamun,<div><br></div><div>This particular motif maps twice in this location; once on the forward and once on the reverse strand. This is not uncommon due to the frequently palindromic nature of the motif sequences.</div>
<div><br></div><div>The VEP unfortunately does not indicate which strand the feature maps to; this will be fixed in the next version of VEP.</div><div><br></div><div>The position is always given counting from the 5' end. You can see how the VEP calculates the position and score delta in the subroutine named motif_score_delta in ensembl-variation/modules/Bio/EnsEMBL/Variation/MotifFeatureVariationAllele.pm</div>
<div><br></div><div>Hope that helps</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote"><div><div class="h5">On 20 February 2014 20:57, Rashid Mamunur <span dir="ltr"><<a href="mailto:rm8@sanger.ac.uk" target="_blank">rm8@sanger.ac.uk</a>></span> wrote:<br>
</div></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5"><div style="word-wrap:break-word"><div>Hi everyone,</div><div><br></div><div>I am trying to predict the predict the effect of a variation on the motif binding affinity. I have extracted the values via VEP.</div>
<div>However to understand the mechanism better, I am trying to compare VEP information with manually (Ensembl FuncGen API) </div><div>extracted information.</div><div><br></div><div>Example : </div><div><span style="color:rgb(178,49,0);font-family:Monaco;font-size:11px">1</span><span style="color:rgb(178,49,0);font-family:Monaco;font-size:11px;white-space:pre-wrap"> </span><span style="color:rgb(178,49,0);font-family:Monaco;font-size:11px">40505680</span><span style="color:rgb(178,49,0);font-family:Monaco;font-size:11px;white-space:pre-wrap"> </span><span style="font-family:Monaco;font-size:11px">T<span style="white-space:pre-wrap"> </span>C</span></div>
<div>For the above genomic location I try to extract motif features and original binding affinity and I get following information :</div><div> </div><div><div style="margin:0px"><div style="font-size:11px;font-family:Monaco;margin:0px">
Srf<span style="color:rgb(193,53,0)">:</span>MA0083<span style="color:rgb(193,53,0)">.</span><span style="color:rgb(178,49,0)">1 </span><span style="color:rgb(193,53,0)">-> </span>GACCATCTATGG | <span style="color:rgb(178,49,0)">40505673 </span>| <span style="color:rgb(178,49,0)">40505684 </span>| <span style="color:rgb(178,49,0)">1 </span>| <span style="color:rgb(178,49,0)">12 </span>| MA0083<span style="color:rgb(193,53,0)">.</span><span style="color:rgb(178,49,0)">1 </span>| affinity<span style="color:rgb(193,53,0)">:<span style="white-space:pre-wrap"> </span></span><span style="color:rgb(178,49,0)">0</span><span style="color:rgb(193,53,0)">.</span><span style="color:rgb(178,49,0)">888415882885811</span></div>
<div style="font-size:11px;font-family:Monaco;margin:0px">Srf<span style="color:rgb(193,53,0)">:</span>MA0083<span style="color:rgb(193,53,0)">.</span><span style="color:rgb(178,49,0)">1 </span><span style="color:rgb(193,53,0)">-> </span>GACCATAGATGG | <span style="color:rgb(178,49,0)">40505675 </span>| <span style="color:rgb(178,49,0)">40505686 </span>| <span style="color:rgb(193,53,0)">-</span><span style="color:rgb(178,49,0)">1 </span>| <span style="color:rgb(178,49,0)">12 </span>| MA0083<span style="color:rgb(193,53,0)">.</span><span style="color:rgb(178,49,0)">1 </span>| affinity<span style="color:rgb(193,53,0)">:<span style="white-space:pre-wrap"> </span></span><span style="color:rgb(178,49,0)">0</span><span style="color:rgb(193,53,0)">.</span><span style="color:rgb(178,49,0)">888745476322399</span></div>
<div style="font-size:11px;font-family:Monaco"><br></div><div>This is an example of same motif in forward and reverse strand. My question is </div><div><b>- if I want to calculate effect of variation, which bases in the above two sequences do I change ??</b></div>
<div><br></div><div>For the same location predicted with VEP, I have the following result : </div><div><div style="margin:0px;font-size:11px;font-family:Monaco"><br></div><div style="margin:0px;font-size:11px;font-family:Monaco">
<span style="white-space:pre-wrap"> </span>MOTIF_POS<span style="color:rgb(193,53,0)">=</span><span style="color:rgb(178,49,0)">7</span><span style="color:rgb(193,53,0)">;</span>MOTIF_NAME<span style="color:rgb(193,53,0)">=</span>Jaspar_Matrix_Srf<span style="color:rgb(193,53,0)">:</span>MA0083<span style="color:rgb(193,53,0)">.</span><span style="color:rgb(178,49,0)">1</span><span style="color:rgb(193,53,0)">;</span>HIGH_INF_POS<span style="color:rgb(193,53,0)">=</span>Y<span style="color:rgb(193,53,0)">;</span>MOTIF_SCORE_CHANGE<span style="color:rgb(193,53,0)">=-</span><span style="color:rgb(178,49,0)">0</span><span style="color:rgb(193,53,0)">.</span><span style="color:rgb(178,49,0)">092</span></div>
<div style="margin:0px;font-size:11px;font-family:Monaco"><span style="white-space:pre-wrap"> </span>MOTIF_POS<span style="color:rgb(193,53,0)">=</span><span style="color:rgb(178,49,0)">8</span><span style="color:rgb(193,53,0)">;</span>MOTIF_NAME<span style="color:rgb(193,53,0)">=</span>Jaspar_Matrix_Srf<span style="color:rgb(193,53,0)">:</span>MA0083<span style="color:rgb(193,53,0)">.</span><span style="color:rgb(178,49,0)">1</span><span style="color:rgb(193,53,0)">;</span>HIGH_INF_POS<span style="color:rgb(193,53,0)">=</span>Y<span style="color:rgb(193,53,0)">;</span>MOTIF_SCORE_CHANGE<span style="color:rgb(193,53,0)">=-</span><span style="color:rgb(178,49,0)">0</span><span style="color:rgb(193,53,0)">.</span><span style="color:rgb(178,49,0)">092</span></div>
</div><div style="margin:0px;font-size:11px;font-family:Monaco"><span style="font-family:Helvetica;font-size:medium"><br></span></div><div style="margin:0px;font-size:11px;font-family:Monaco"><span style="font-family:Helvetica;font-size:medium">As VEP output does not give any strand information, I am struggling to map the VEP outputs to the motifs extracted via FuncGen;</span></div>
<div style="margin:0px">- which positions in the original motif sequence does the <span style="font-family:Monaco;font-size:11px">MOTIF_POS </span>values corresponds to ??</div><div style="margin:0px"><br></div><div style="margin:0px">
Apology in advance for such a long question. </div><div style="margin:0px"><br></div><div style="margin:0px">Thanks in advance.</div><div style="margin:0px"><br></div><div style="margin:0px">Mamun</div></div></div></div>
<br></div></div>
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