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A widely used collection of programs for thermodynamic RNA secondary structure prediction. Over the years, many additional tools have been developed building on the core programs of the package to also address issues related to noncoding RNA detection, RNA folding kinetics, or efficient sequence design considering RNA-RNA hybridizations. The ViennaRNA web services provide easy and user-friendly web access to these tools.
PairFold
Predicts the secondary structure of a pair of RNA or DNA molecules. Extending the notion of secondary structure for a single molecule, a secondary structure for a pair of molecules (R1, R2) is a set of base pairs, with each base of R1 and R2 occurring in at most one pair. The model for measuring the free energy of a secondary structure for two DNA or RNA molecules at a given temperature is very similar to that for a single molecule, except that a intermolecular initiation penalty is added.
aRNhAck
Assists users in analyzing non-coding RNA sequences. ARNhAck provides a software that focuses on the sole biochemical and evolutionary properties of the RNA. It gathers biochemical signal from structure probing experiments on RNA mutants with evolutionary information, collected in multiple sequence alignments (MSAs). The method intends to help in the identification, without prior knowledge of potential partners and hot-spots in RNA, involved in RNA–RNA, RNA–Protein, RNA–DNA and RNA–ligand interfaces.
RIsearch
Searches fast RNA-RNA interaction. RIsearch employs a modified Smith-Waterman-Gotoh algorithm based on di-nucleotides to approximate nearest-neighbor energy parameters. The software focuses on perfect-complementary seed regions and extends them on both-ends. It also allows to locate microRNA (miRNA) target sites in genomic sequence. Used as a pre-filter, the software reduces the number of binding site candidates reported by miRNA target prediction programs. Using RIsearch as a pre-filter in genome-wide screens reduces the number of binding site candidates reported by miRNA target prediction programs, such as TargetScanS and miRanda, by up to 70%.
LRIscan / Long-range RNA-RNA interactions scan
A tool for the Long-range RNA-RNA interactions (LRI) prediction in full viral genomes based on a multiple genome alignment. LRIscan offers the opportunity to predict possible LRIs under certain criteria and reduces dramatically the number of candidates for wet lab studies. 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.
RactIPAce / RNA– RNA interACTions Integer Programming AcCEssibility
A based prediction model of RNA-RNA interactions. RactIPAce achieves the best predictive performance on the newly compiled dataset of experimentally verified interactions in the literature as compared with the state-of-the-art methods. It is a highly improved version of RactIP that incorporates precomputed AcCEssibility as well as a new hybridization energy model by extending the previous IP formulation. RactIPAce can be effective to predict interaction sites after screening for real interacting RNAs, which will boost the functional analysis of regulatory RNAs.
EPLMI
Predicts new lncRNA-miRNA interactions and computes the putative interaction strength of known lncRNA-miRNA interactions. EPLMI is based on known lncRNA-miRNA interaction network. It can be useful for measuring the competitiveness of lncRNAs identified to interact with specific miRNAs. This tool can yield important insights into future research on ceRNA regulation networks. It can make its predictions by using collaborative effects of both lncRNAs and miRNAs and the similarities of lncRNAs and miRNAs.
circlncRNAnet
Maps the functional networks of long or circular forms of non-coding RNAs (ncRNA). circlncRNAnet allows in-depth analyses of ncRNA biology. The software provides three features: (1) a framework for processing of user-defined next-generation sequencing (NGS)-based expression data, (2) assigning and assessing the regulatory networks of ncRNAs selected by users and (3) a workflow suitable for all types of ncRNAs. It can be used to get multiple lines of functionally relevant information on the circular RNA/ long non-coding RNA (circRNAs/lncRNAs) of users’ interest.
IRBIS / Intermolecular RNA (BLAT-like) Interaction Search
A computational pipeline for detecting conserved complementary regions in unaligned orthologous sequences. Unlike other methods, IRBIS follows the "first-fold-then-align" principle in which all possible combinations of complementary k-mers are searched for simultaneous conservation. The novel trimming procedure reduces the size of the search space and improves the performance to the point where large-scale analyses of intra- and intermolecular RNA-RNA interactions become possible.
ASSA / Antisense Search Approach
Concerns the thermodynamics-based prediction of the RNA-RNA interactions on a transcriptome scale. The general idea of Antisense Search Approach (ASSA) is to first identify putative antisense sites by the local sequence alignment tool BLASTn, compute the interaction energy (∆∆G) for each site by the RNA co-folding tool bifold and using the obtained ∆∆G values estimate the statistical significance of each predicted RNA-RNA interaction. It uses the thermodynamics algorithm bifold for a transcriptome-wide prediction of RNA-RNA interactions.
RIblast
A package to predict RNA-RNA interaction. RIblast is based on seed-and-extension algorithm for comprehensive lncRNA interactome analysis. It consists of database construction search step and RNA interaction search step. RIblast discovers seed regions using suffix arrays and subsequently extends seed regions based on an RNA secondary structure energy model. Computational experiments indicate that RIblast achieves a level of prediction accuracy similar to those of existing programs, but at speeds over 64 times faster than existing programs.
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RAID / RNA Association Interaction Database
Provides RNA-associated (RNA-RNA/RNA-protein) interaction database. RAID intends to provide the scientific community with all-in-one resources for efficient browsing and extraction of the RNA-associated interactions. RAID integrates experimental and computational prediction interactions from manually reading literature and other database resources under one common framework. The new developments in RAID include (i) over 850-fold RNA-associated interactions, an enhancement compared to the previous version; (ii) numerous resources integrated with experimental or computational prediction evidence for each RNA-associated interaction; (iii) a reliability assessment for each RNA-associated interaction based on an integrative confidence score; and (iv) an increase of species coverage to 60.
RISE / RNA Interactome from Sequencing Experiments
Provides RNA-RNA interactions (RRIs) identified through high-throughput sequencing technologies. RISE is a comprehensive database of RNA interactome from sequencing experiments. It includes (i) comprehensive curation of RRIs, (ii) a large dataset of RRIs among mRNAs and lncRNAs, (iii) details of the interacting sites and (iv) extensive annotations for each RRI. It provides an assistance for researchers looking for interaction and other functional information on individual RNAs, and analyzing RRI networks of specific pathways or systems.
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