Protein-specific prediction of mRNA binding using RNA sequences, binding motifs and predicted secondary structures.

ABSTRACT:

Background

RNA-binding proteins interact with specific RNA molecules to regulate important cellular processes. It is therefore necessary to identify the RNA interaction partners in order to understand the precise functions of such proteins. Protein-RNA interactions are typically characterized using in vivo and in vitro experiments but these may not detect all binding partners. Therefore, computational methods that capture the protein-dependent nature of such binding interactions could help to predict potential binding partners in silico.

Results

We have developed three methods to predict whether an RNA can interact with a particular RNA-binding protein using support vector machines and different features based on the sequence (the Oli method), the motif score (the OliMo meth

SUBMITTER: Livi CM 

PROVIDER: S-EPMC4098778 | biostudies-literature | 2014 Apr

REPOSITORIES: biostudies-literature