Prediction of conserved long-range RNA-RNA interactions in full viral genomes.

ABSTRACT:

Motivation

Long-range RNA-RNA interactions (LRIs) play an important role in viral replication, however, only a few of these interactions are known and only for a small number of viral species. Up to now, it has been impossible to screen a full viral genome for LRIs experimentally or in silico Most known LRIs are cross-reacting structures (pseudoknots) undetectable by most bioinformatical tools.

Results

We present LRIscan, a tool for the LRI prediction in full viral genomes based on a multiple genome alignment. We confirmed 14 out of 16 experimentally known and evolutionary conserved LRIs in genome alignments of HCV, Tombusviruses, Flaviviruses and HIV-1. We provide several promising new interactions, which include compensatory mutations and are highly conserved in all consid

SUBMITTER: Fricke M 

PROVIDER: S-EPMC7189868 | biostudies-literature | 2016 Oct

REPOSITORIES: biostudies-literature