<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><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 class="Apple-tab-span" style="color: rgb(178, 49, 0); font-family: Monaco; font-size: 11px; white-space: pre; "> </span><span style="color: rgb(178, 49, 0); font-family: Monaco; font-size: 11px; ">40505680</span><span class="Apple-tab-span" style="color: rgb(178, 49, 0); font-family: Monaco; font-size: 11px; white-space: pre; "> </span><span style="font-family: Monaco; font-size: 11px; ">T<span class="Apple-tab-span" style="white-space: pre; "> </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 class="Apple-tab-span" style="white-space: pre; "> </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 class="Apple-tab-span" style="white-space: pre; "> </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 class="Apple-tab-span" style="white-space: pre; "> </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 class="Apple-tab-span" style="white-space: pre; "> </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></body></html>