[ensembl-dev] Predicting Motif Score Change
Rashid Mamunur
rm8 at sanger.ac.uk
Thu Feb 20 20:57:38 GMT 2014
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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20140220/79b15176/attachment.html>
More information about the Dev
mailing list