Position-specific evolution in transcription factor binding sites, and a fast likelihood calculation for the F81 model
Pavitra Selvakumar,
Rahul Siddharthan
Abstract:Transcription factor binding sites (TFBS), like other DNA sequence, evolve via mutation and selection relating to their function. Models of nucleotide evolution describe DNA evolution via single-nucleotide mutation. A stationary vector of such a model is the long-term distribution of nucleotides, unchanging under the model. Neutrally evolving sites may have uniform stationary vectors, but one expects that sites within a TFBS instead have stationary vectors reflective of the fitness of various nucleotides at th… Show more
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