Here we present a new sequence-based computational method to predict the effect of regulatory variation, using a classifier (gkm-SVM) which encodes cell-specific regulatory sequence vocabularies. The induced change in the gkm-SVM score, deltaSVM, quantifies the effect of variants.
Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer MA. 2015. A method to predict the impact of regulatory variants from DNA sequence. Nat Genet. advance online publication. doi:10.1038/ng.3331
http://www.beerlab.org/deltasvm/
Here we present a new sequence-based computational method to predict the effect of regulatory variation, using a classifier (gkm-SVM) which encodes cell-specific regulatory sequence vocabularies. The induced change in the gkm-SVM score, deltaSVM, quantifies the effect of variants.
Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer MA. 2015. A method to predict the impact of regulatory variants from DNA sequence. Nat Genet. advance online publication. doi:10.1038/ng.3331