ArticleBioinformatics (Oxford, England)2016
Prediction of conserved long-range RNA-RNA interactions in full viral genomes.
Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 16 citations in OpenAlex.
- A potential RNA-RNA distal interaction competing with a functional pseudoknot in the 3'-untranslated region of SARS-like coronaviruses.Nucleic acids research · 2026Article
- Viral non-coding RNA structure annotation and API-based data retrieval with Rfam and R2DT.bioRxiv : the preprint server for biology · 2026Article
- First full-genome alignment representative for the genusRNA (New York, N.Y.) · 2026Article
- MMTV RNA packaging requires an extended long-range interaction for productive Gag binding to packaging signals.PLoS biology · 2024Article
- Regulation viral RNA transcription and replication by higher-order RNA structures within the nsp1 coding region of MERS coronavirus.Scientific reports · 2024Article
- Women in the European Virus Bioinformatics Center.Viruses · 2022Article
- Hepatitis C Virus Translation Regulation.International journal of molecular sciences · 2020Review
- The Role of the RNA-RNA Interactome in the Hepatitis C Virus Life Cycle.International journal of molecular sciences · 2020Review
- Article
- Review
- Intragenomic Long-Distance RNA-RNA Interactions in Plus-Strand RNA Plant Viruses.Frontiers in microbiology · 2018Review
- Signals Involved in Regulation of Hepatitis C Virus RNA Genome Translation and Replication.Frontiers in microbiology · 2018Review
- Software Dedicated to Virus Sequence Analysis "Bioinformatics Goes Viral".Advances in virus research · 2017Article
- Know Your Enemy: Successful Bioinformatic Approaches to Predict Functional RNA Structures in Viral RNAs.Frontiers in microbiology · 2017Review
- Synonymous Co-Variation across the E1/E2 Gene Junction of Hepatitis C Virus Defines Virion Fitness.PloS one · 2016Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationLong-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.
resultsWe 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. AVAILABILITY AND IMPLEMENTATION: 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. CONTACT: manja@uni-jena.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.