[ensembl-dev] Predicting Motif Score Change

[Will McLaren]

Sorry, here's a link to the module documentation:

http://www.ensembl.org/info/docs/Doxygen/variation-api/classBio_1_1EnsEMBL_1_1Variation_1_1MotifFeatureVariationAllele.html#ac830653283dfdb6b85305373cc6a4d98


On 25 February 2014 14:35, Will McLaren <wm2 at ebi.ac.uk> wrote:

> 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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>>
>
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