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 4.1.1

Freiburg RNA Tools

Freiburg RNA tools provides online access to a series of RNA research tools developed by the Freiburg Bioinformatics Group for sequence-structure alignments (LocARNA, CARNA, MARNA), clustering (ExpaRNA), interaction prediction (IntaRNA, CopraRNA), 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.

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.

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.

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.

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.

CPSP-Tools for Lattice Protein Models

CPSP-Tools are a collections of programs to solve the problems typical of studies using 3D lattice protein models. Among the tasks addressed are the prediction of globally optimal and/or suboptimal structures as well as sequence design and neutral network exploration.