Inherent limitations of probabilistic models for protein-DNA binding specificity.

ABSTRACT: The specificities of transcription factors are most commonly represented with probabilistic models. These models provide a probability for each base occurring at each position within the binding site and the positions are assumed to contribute independently. The model is simple and intuitive and is the basis for many motif discovery algorithms. However, the model also has inherent limitations that prevent it from accurately representing true binding probabilities, especially for the highest affinity sites under conditions of high protein concentration. The limitations are not due to the assumption of independence between positions but rather are caused by the non-linear relationship between binding affinity and binding probability and the fact that independent normalization at each positio

SUBMITTER: Ruan S 

PROVIDER: S-EPMC5521849 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature