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


  • Source and binaries of LRIscan (Linux) [tar.gz]
  • Binaries of LRIscan (Windows) [exe]
  • Manual [PDF]

LRIscan input alignments

LRIscan output sample

LRIscan runtime for sample data

sample #seq runtime
 Flavivirus  6 ~ 14 min
 HCV  106 ~ 314 min
 Tombusvirus  13 ~ 26 min
 HIV-1  200 ~ 583 min


(Download .bib)
title = {Prediction of conserved long-range RNA-RNA interactions in full viral genomes},
author = {Fricke M and Marz M},
url = {},
doi = {10.1093/bioinformatics/btw323},
issn = {1367-4811},
year  = {2016},
date = {2016-06-10},
journal = {Bioinformatics (Oxford, England)},
abstract = {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.},