[ensembl-dev] Predicting Motif Score Change

[Will McLaren]

Hello Mamun,

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.

The VEP unfortunately does not indicate which strand the feature maps to;
this will be fixed in the next version of VEP.

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

Hope that helps

Will McLaren
Ensembl Variation


On 20 February 2014 20:57, Rashid Mamunur <rm8 at sanger.ac.uk> wrote:

> Hi everyone,
>
> I am trying to predict the predict the effect of a variation on the motif
> binding affinity. I have extracted the values via VEP.
> However to understand the mechanism better, I am trying to compare VEP
> information with manually (Ensembl FuncGen API)
> extracted information.
>
> Example :
> 1 40505680 T C
> For the above genomic location I try to extract motif features and
> original binding affinity and I get following information :
>
> Srf:MA0083.1 -> GACCATCTATGG | 40505673 | 40505684 | 1 | 12 | MA0083.1 |
> affinity: 0.888415882885811
> Srf:MA0083.1 -> GACCATAGATGG | 40505675 | 40505686 | -1 | 12 | MA0083.1 |
> affinity: 0.888745476322399
>
> This is an example of same motif in forward and reverse strand. My
> question is
> *- if I want to calculate effect of variation, which bases in the above
> two sequences do I change ??*
>
> For the same location predicted with VEP, I have the following result  :
>
> MOTIF_POS=7;MOTIF_NAME=Jaspar_Matrix_Srf:MA0083.1;HIGH_INF_POS=Y;
> MOTIF_SCORE_CHANGE=-0.092
> MOTIF_POS=8;MOTIF_NAME=Jaspar_Matrix_Srf:MA0083.1;HIGH_INF_POS=Y;
> MOTIF_SCORE_CHANGE=-0.092
>
> As VEP output does not give any strand information, I am struggling to map
> the VEP outputs to the motifs extracted via FuncGen;
> - which positions in the original motif sequence does the MOTIF_POS values
> corresponds to ??
>
> Apology in advance for such a long question.
>
> Thanks in advance.
>
> Mamun
>
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