SSMART: sequence-structure motif identification for RNA-binding proteins.

ABSTRACT:

Motivation

RNA-binding proteins (RBPs) regulate every aspect of RNA metabolism and function. There are hundreds of RBPs encoded in the eukaryotic genomes, and each recognize its RNA targets through a specific mixture of RNA sequence and structure properties. For most RBPs, however, only a primary sequence motif has been determined, while the structure of the binding sites is uncharacterized.

Results

We developed SSMART, an RNA motif finder that simultaneously models the primary sequence and the structural properties of the RNA targets sites. The sequence-structure motifs are represented as consensus strings over a degenerate alphabet, extending the IUPAC codes for nucleotides to account for secondary structure preferences. Evaluation on synthetic data showed that SSMART is a

SUBMITTER: Munteanu A 

PROVIDER: S-EPMC6247937 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature