RNAcontext: a new method for learning the sequence and structure binding preferences of RNA-binding proteins.

ABSTRACT: Metazoan genomes encode hundreds of RNA-binding proteins (RBPs). These proteins regulate post-transcriptional gene expression and have critical roles in numerous cellular processes including mRNA splicing, export, stability and translation. Despite their ubiquity and importance, the binding preferences for most RBPs are not well characterized. In vitro and in vivo studies, using affinity selection-based approaches, have successfully identified RNA sequence associated with specific RBPs; however, it is difficult to infer RBP sequence and structural preferences without specifically designed motif finding methods. In this study, we introduce a new motif-finding method, RNAcontext, designed to elucidate RBP-specific sequence and structural preferences with greater accuracy than existing approa

SUBMITTER: Kazan H 

PROVIDER: S-EPMC2895634 | biostudies-literature | 2010 Jul

REPOSITORIES: biostudies-literature