Hello Everyone,
I have a question and I hope some of you have some idea or possible solutions to this problem:
It has been publish that enhancers regions undergo suboptimization, which means motifs for certain region have reduced binding affinities, in the paper they test this hypothesis mostly experimentally by introducing mutations in flaking sites of the enhancer and test how this affects expression, also comparisons between matrices of MOTIFs for TMS and cloned and sequenced regulatory regions.
Which bioinformatic method would you suggest to find Motif "suboptimization" across several peaks from chip-seq experiments and ponderate each region based on its variations, I have made some work in finding motifs with classic programs but I don't know how to do it massively or more detailed.
Thank you very much, Carlos
Paper: http://science.sciencemag.org/content/sci/350/6258/325.full.pdf
