RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets.

ABSTRACT: Intermolecular interactions of ncRNAs are at the core of gene regulation events, and identifying the full map of these interactions bears crucial importance for ncRNA functional studies. It is known that RNA-RNA interactions are built up by complementary base pairings between interacting RNAs and high level of complementarity between two RNA sequences is a powerful predictor of such interactions. Here, we present RIsearch2, a large-scale RNA-RNA interaction prediction tool that enables quick localization of potential near-complementary RNA-RNA interactions between given query and target sequences. In contrast to previous heuristics which either search for exact matches while including G-U wobble pairs or employ simplified energy models, we present a novel approach using a single integrated

SUBMITTER: Alkan F 

PROVIDER: S-EPMC5416843 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature