A Package For Predicting The Disruptiveness Of Single Nucleotide
Polymorphisms On Transcription Factor Binding Sites
Description
We introduce motifbreakR, which allows the biologist to
judge in the first place whether the sequence surrounding the
polymorphism is a good match, and in the second place how much
information is gained or lost in one allele of the polymorphism
relative to another. MotifbreakR is both flexible and
extensible over previous offerings; giving a choice of
algorithms for interrogation of genomes with motifs from public
sources that users can choose from; these are 1) a weighted-sum
probability matrix, 2) log-probabilities, and 3) weighted by
relative entropy. MotifbreakR can predict effects for novel or
previously described variants in public databases, making it
suitable for tasks beyond the scope of its original design.
Lastly, it can be used to interrogate any genome curated within
Bioconductor (currently there are 22).