RCK: accurate and efficient inference of sequence- and structure-based protein-RNA binding models from RNAcompete data.

ABSTRACT:

Motivation

Protein-RNA interactions, which play vital roles in many processes, are mediated through both RNA sequence and structure. CLIP-based methods, which measure protein-RNA binding in vivo, suffer from experimental noise and systematic biases, whereas in vitro experiments capture a clearer signal of protein RNA-binding. Among them, RNAcompete provides binding affinities of a specific protein to more than 240 000 unstructured RNA probes in one experiment. The computational challenge is to infer RNA structure- and sequence-based binding models from these data. The state-of-the-art in sequence models, Deepbind, does not model structural preferences. RNAcontext models both sequence and structure preferences, but is outperformed by GraphProt. Unfortunately, GraphProt cannot detect

SUBMITTER: Orenstein Y 

PROVIDER: S-EPMC4908343 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature