On the value of intra-motif dependencies of human insulator protein CTCF.

ABSTRACT: The binding affinity of DNA-binding proteins such as transcription factors is mainly determined by the base composition of the corresponding binding site on the DNA strand. Most proteins do not bind only a single sequence, but rather a set of sequences, which may be modeled by a sequence motif. Algorithms for de novo motif discovery differ in their promoter models, learning approaches, and other aspects, but typically use the statistically simple position weight matrix model for the motif, which assumes statistical independence among all nucleotides. However, there is no clear justification for that assumption, leading to an ongoing debate about the importance of modeling dependencies between nucleotides within binding sites. In the past, modeling statistical dependencies within binding si

SUBMITTER: Eggeling R 

PROVIDER: S-EPMC3899044 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature