Freiburg RNA Tools


This web server provides online access to a series of tools developed by the Freiburg Bioinformatics Group. To start using it, please select from the listings below, or use the menu on the left. If you prefer doing a local installation on your machine, please visit our 'Download' section.

If you use our tools for research or education, please cite the corresponding articles from the 'Publications' section.

Version 5.0.10

Freiburg RNA Tools

Freiburg RNA tools provides online access to a series of RNA research tools developed by the Freiburg Bioinformatics Group and colleagues for sequence-structure alignments (LocARNA, CARNA, MARNA), clustering (ExpaRNA), interaction prediction (IntaRNA, CopraRNA, metaMIR), identification of homologs (GLASSgo), sequence design (AntaRNA, INFORNA, SECISDesign), CRISPR repeat analyses (CRISPRmap), and many more tasks.

Interaction Prediction

CopraRNA is a tool for sRNA target prediction. It computes whole genome predictions by combination of whole genome IntaRNA predictions using homologous sRNA sequences from distinct organisms.

IntaRNA enables the prediction of RNA-RNA interactions. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions.

GLASSgo (GLobal Automated sRNA Search go) combines iterative BLAST searches, pairwise identity filtering, and structure based clustering in an automated prediction pipeline to find sRNA homologs from scratch. The web server provides predefined parameter sets for a non-expert usage as well as enables a manual setup of the query parameters.

metaMIR is a microRNA (miRNA) framework to predict interactions in human between miRNAs and clusters of genes. The user provides a set of genes to be targeted, and optionally genes not to be targeted. Taking data from a reference database of previously established predictive algorithms, metaMIR will return miRNA candidates predicted to co-regulate genes among those entered by analyzing all possible subset combinations.

Seq-Str Alignment

LocARNA computes multiple alignments of RNAs based on their sequence and structure similarity. In contrast to, e.g. MARNA, it considers the whole ensemble of secondary structures for each RNA. Thus, LocARNA aligns RNAs with unknown structure and predicts a consensus secondary structure for a set of unaligned RNAs. Specification of additional constraints or even enforcement of fixed input structures is possible. LocARNA is best suited to compare structural RNAs, in particular, of low sequence similarity.

Carna is a tool for multiple alignment of RNA molecules based on their full ensembles of structures. Carna computes the alignment that fits best to all likely structures simultaneously. Hence, Carna is in particular useful to align RNAs with more than one stable structure, as for example riboswitches, and is able to align arbitrary pseudoknots.

MARNA computes multiple sequence-structure alignments considering a single fixed structure for each sequence only.

ExpaRNA is a fast, motif-based comparison and alignment tool for RNA molecules. Instead of computing a full sequence-structure alignment, it computes the best arrangement of sequence-structure motifs common to two RNAs.


CRISPRmap provides a quick and detailed insight into repeat conservation and diversity of both bacterial and archaeal systems. It comprises the largest dataset of CRISPRs to date and enables comprehensive independent clustering analyses to determine conserved sequence families, potential structure motifs for endoribonucleases, and evolutionary relationships.

CRISPRloci provides an automated and comprehensive in silico characteriztion of CRISPR-Cas system on bacterial and archaeal genomes. It is a full suite for CRISPR locus characteriztion that includes CRISPR array orientation, detection of conserved leaders, cas gene annotation and subtype classification.

Sequence Design

AntaRNA is an Ant-Colony Optimization based tool which solves the RNA inverse folding problem. It designs RNA sequences which satisfy a set of constraints made by the user. The realized multi-objective optimization allows to introduce structure, sequence and GC-content constraints.

INFO-RNA is a server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.

SECISDesign is a server for the design of SECIS-elements within the coding sequence of an mRNA with both structure and sequence constraints. Furthermore, a certain similarity to the original protein is kept. It can be used e.g. for recombinant expression of selenoproteins in E. coli.


NIPU allows to display splicing regulatory motifs and single-stranded regions.

SNP & Mutation

CopomuS rates and ranks possible compensatory mutations of IntaRNA predictions to support the design of verification experiments for putative RNA-RNA interactions.

MutaRNA (Mutational Analysis of RNAs) predicts and visualizes the mutation-induced structure changes of a single-nucleotide polymorphism (SNP) in an RNA sequence. This covers changes in the accessibility (single-strandedness) of the molecule, its intra-molecular base pairing potential and its the base pairing probabilities. Combined with evaluation results of tools like remuRNA and RNAsnp, MutaRNA enables a detailed evaluation of a mutation's effects on RNA structure formation.

(offline) RaSE uses the graph vectorization technique of EDeN to compute a score indicative of the structural stability responsibility of each nucleotide in an RNA sequence. The score is computed as the similarity of the structure obtained by changing a single nucleotide with respect to the original structure. The structure is based on RNAplfold base pair probabilities and thus reflects the overall structural ensemble accessible to the RNA molecule. Per sequence position, only the mutation which yields the largest structural difference is reported.


BrainDead learns a two-class model for short RNA sequences based on accessibility-enhanced k-mer features and applies it for class prediction of unknown RNAs.

Gene set extension

Given a list of genes known to be associated with a given genetic disease, DiGI predicts and ranks a list of unknown genes based on their probabilities to be related to that disease.

Teaching RNA algorithms

In order to enable an example-driven learning and teaching of RNA structure related algorithms, we provide here Javascript-based implementations for various algorithms for RNA structure and RNA-RNA interaction prediction. To reduce the level of complexity, all algorithms use a simple Nussinov-like energy scoring scheme, i.e. the energy of an RNA structure is directly related to its number of base pairs without further distinction.
Furthermore, we provide interactive implementations for general sequence alignment algorithms that are taught in our bioinformatics courses.
The source code of all implementations is available

The Freiburg Bioinformatics Group also provides:

MoDPepInt Server

MoDPepInt (Modular Domain Peptide Interaction) is a simple and interactive webserver, which comprises three different tools, i.e. SH2PepInt, SH3PepInt and PDZPepInt, for predicting the binding partners of three different modular protein domains, i.e. SH2, SH3 and PDZ domains, respectively.

CPSP-Tools Server

CPSP (Constraint-based Protein Structure Prediction) is an exact and efficient approach to identify optimal structures of lattice proteins within the hydrophobic-polar (HP) model. The approach enables structure prediction within the 3D cubic and 3D face-centered-cubic (FCC) lattice for both backbone-only as well as side-chain representing models.

Galaxy Project - Uni Freiburg

The Freiburg Galaxy Team offers a framework for scientists on e.g. NGS data analyses (RNA-seq, ChIP-seq, Exome-seq, MethylC-seq), genome annotation analyses for eukaryotic and prokaryotic organisms (from gene prediction to functional description), Proteomics and Metabolomics analysis, and the ChemicalToolBoX for analysis of small compounds. Galaxy contains more than 800 different single analysis tools and ready-to-use pipelines for different applications.

The Freiburg Galaxy Project is part of the “German Network for Bioinformatics Infrastructure” (Deutsches Netzwerk für Bioinformatik-Infrastruktur, de.NBI) and the Collaborative Research Centre (CRC) 992 for Medical Epigenetics and offers within the RNA Bioinformatic Centre (RBC) a central platform for RNA analysis.

CMV server

CMV server
CMV (co-variance model visualization) offers tools for the visualization of RNA family models, also known as co-variance models (CM) and Hidden Markov Models (HMM). Moreover, comparisons between models, the multiple sequence alignments they were constructed from and, in the case of RNA families, the consensus secondary structure can be visualized. The aim is to simplify model construction and evaluation by providing visualizations with different levels of detail.