SMARTIV: combined sequence and structure de-novo motif discovery for in-vivo RNA binding data.

ABSTRACT: Gene expression regulation is highly dependent on binding of RNA-binding proteins (RBPs) to their RNA targets. Growing evidence supports the notion that both RNA primary sequence and its local secondary structure play a role in specific Protein-RNA recognition and binding. Despite the great advance in high-throughput experimental methods for identifying sequence targets of RBPs, predicting the specific sequence and structure binding preferences of RBPs remains a major challenge. We present a novel webserver, SMARTIV, designed for discovering and visualizing combined RNA sequence and structure motifs from high-throughput RNA-binding data, generated from in-vivo experiments. The uniqueness of SMARTIV is that it predicts motifs from enriched k-mers that combine information from ranked RNA seq

SUBMITTER: Polishchuk M 

PROVIDER: S-EPMC6030986 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature