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



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 considered viral sequences. Furthermore, we provide reactivity plots highlighting the hot spots of predicted LRIs.



Source code and binaries of LRIscan freely available for download at http://www.rna.uni-jena.de/en/supplements/lriscan/, implemented in Ruby/C ++ and supported on Linux and Windows.



manja@uni-jena.de



Supplementary data are available at Bioinformatics online.
Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.
Markus
M
Fricke
Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany FLI Leibniz Institute for Age Research, Jena, Germany.
Manja
M
Marz
D003198:Computer Simulation; D016679:Genome, Viral; D012367:RNA, Viral; D017423:Sequence Analysis, RNA; D012984:Software
D012367:RNA, Viral