SSMART: Sequence-structure motif identification for RNA-binding proteins

Item Type:

Article

Title:

Creators Name:

Munteanu, A. and Mukherjee, N. and Ohler, U.

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 able to recover both sequence and structure motifs implanted into 3'UTR-like sequences, for various degrees of structured/unstructured binding sites. In addition, we successfully used SSMART on high-throughput in vivo and in vitro data, showing that we not only recover the known sequence motif, but also gain insight into the structural preferences of the RBP. AVAILABILITY: SSMART is freely available at https://ohlerlab.mdc-berlin.de/software/SSMART_137/.

Keywords:

Binding Sites, Computational Biology, Nucleotide Motifs, RNA, RNA-Binding Proteins, RNA Sequence Analysis, Software

Source:

Bioinformatics

ISSN:

1367-4803

Publisher:

Oxford University Press

Volume:

Number:

Page Range:

3990-3998

Date:

1 December 2018

Official Publication:

https://doi.org/10.1093/bioinformatics/bty404

External Fulltext:

View full text on PubMed Central

PubMed:

View item in PubMed

Related to:

URL	URL Type
https://edoc.mdc-berlin.de/17346/	Preprint version

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