Institute of Computer Science
University Freiburg



Freiburg RNA tools
RNA related tools from the Freiburg Bioinformatics Group
CRISPR repeat conservation and diversity analysis
• CopraRNA
sRNA target prediction utilizing homology (» download)
• GLASSgo Automated sRNA homolog identification New!
• IntaRNA RNA-RNA interaction prediction (» download) (» movie)
• metaMIR human miRNA-gene interactions New! (» download)
• LocARNA Global and local alignment of RNAs (» download) (» movie)
Alignment of structure ensembles (» download)
• MARNA Fixed structure alignment (» download)
• ExpaRNA Exact matching of sequence-structure motives (» download) (» movie)
• AntaRNA Multi-objective sequence design (» download)
• INFO-RNA Inverse folding of RNA /
Sequence Design
(» download)
• SECISDesign Insert SECIS-elements in coding mRNAs
• NIPU Splicing of regular motifs
RNA motif

Multiple Alignment of RNAs
MoDPepInt Server
Modular domain-peptide interaction tools from the Freiburg Bioinformatics Group
• SH2PepInt
SH2-peptide interaction prediction
• SH3PepInt
SH3-peptide interaction prediction
• PDZPepInt
PDZ-peptide interaction prediction
CPSP web tools
Tools for lattice proteins in the HP-model in various lattice.
• HPstruct Optimal structure prediction (» download)
• HPview Structure visualization (» download)
• LatFit Lattice models of PDB structures (» download)
FCC-HP protein

Software developed within the Freiburg Galaxy Project

A variety of different tools that can be installed and used inside the Galaxy. Many tools are already included in the Galaxy Tool Shed. Galaxy logo
The Galaxy Docker Image is an easy distributable full-fledged Galaxy installation, that can be used for testing, teaching and presenting new tools and features. Docker logo
The RNA workbench is Galaxy Docker instance specifically set up for high throughput RNA analyses. It is developed by the RNA Bioinformatics Center, which is part of the German Network for Bioinformatics Infrastructure (de.NBI). Bioinf Freiburg logo
This projects integrates IPython Notebook, a interactive computational environment, with Galaxy. We hope to make Galaxy more attractive for bioinformaticians and to combine the power of both projects to unlock creativity in data analysis, but also in Next-Generation-Training courses. Check this Galaxy IPython Video to get an idea of its potential. IPython logo

Software and Libraries for Download

metaMIR - a framework to predict in human interactions between microRNAs (miRNA) and clusters of genes metaMIR logo
SPARSE - A simultaneous alignment and folding tool with quadratic complexity
antaRNA - Ant Colony Optimized RNA Sequence Design
EDeN - Explicit Decomposition with Neighborhoods

The Explicit Decomposition with Neighborhoods (EDeN) is a decompositional kernel based on the Neighborhood Subgraph Pairwise Distance Kernel (NSPDK) that can be used to induce an explicit feature representation for graphs. This in turn allows the adoption of machine learning algorithm to perform supervised and unsupervised learning task in a scalable way (e.g. fast stochastic gradient descent methods in classification).
Among the novelties introduced in EDeN is the ability to take in input real vector labels and to process weighted graphs.

BlockClust is an efficient approach to detect transcripts with similar processing patterns. We propose a novel way to encode expression profiles in compact discrete structures, which can then be processed using fast graph-kernel techniques. BlockClust allows both clustering and classification of small non-coding RNAs.

BlockClust runs in three operating modes:
  1. Pre-processing - converts given mapped reads (BAM) into BED file of tags
  2. Clustering and classification - of given input blockgroups (output of blockbuster tool) as explained in the original paper.
  3. Post-processing - plots for overview of predicted clusters.

For a thorough analysis of your data, we suggest you to use complete blockclust workflow, which contains all three modes of operation.

BlockClust Galaxy tool is available in the Galaxy toolshed. BlockClust complete Galaxy workflow with all three operating modes is also available in the toolshed.
CAM - Constraint-based Atom-Atom Mapping ITS - imaginary transition state
ExpaRNA-P - Simultaneous Exact Pattern Matching and Folding of RNAs
GraphProt - modeling binding preferences of RNA-binding proteins
GraphClust - Large Scale structural clustering of RNA sequences (download).
LocalFold - Local Folding of RNA source code distribution
CopraRNA source code bundle for local installation:
IntaRNA - efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites

During the last few years, several new small regulatory RNAs (sRNAs) have been discovered in bacteria. Most of them act as post-transcriptional regulators by base pairing to a target mRNA, causing translational repression or activation, or mRNA degradation. Numerous sRNAs have already been identified, but the number of experimentally verified targets is considerably lower. Consequently, computational target prediction is in great demand. Many existing target prediction programs neglect the accessibility of target sites and the existence of a seed, while other approaches are either specialized to certain types of RNAs or too slow for genome-wide searches.

IntaRNA, developed by Prof. Backofen's bioinformatics group at Freiburg University, is a general and fast approach to the prediction of RNA-RNA interactions incorporating both the accessibility of interacting sites as well as the existence of a user-definable seed interaction. We successfully applied IntaRNA to the prediction of bacterial sRNA targets and determined the exact locations of the interactions with a higher accuracy than competing programs.

For detailed usage information and source code access, refer to IntaRNA @github.

For ad hoc usage, refer to IntaRNA @Freiburg RNA tools.

IntaRNA can be most easily installed locally via badge using

conda install intarna

See Bioconda for further details.

You can download the IntaRNA source code packages (as well as precompiled binaries) from IntaRNA-releases @github.

If you use IntaRNA, please cite our IntaRNA articles.

LocARNA - Global and Local Alignment of RNA.
A tool for pairwise and multiple, global and local alignment of RNA with simultaneous folding. LocARNA requires only RNA sequences as input and will simultaneously fold and align the input sequences. Specifications of additional constraints or fixed input structures are possible. For the folding it makes use of a very realistic energy model for RNAs as it is by RNAfold of the Vienna RNA package (or Zuker's mfold). For the alignment it features RIBOSUM-like similarity scoring and realistic gap cost.
CARNA - alignment of RNA structure ensembles.
CARNA is a tool for multiple alignment of RNA molecules. CARNA requires only the RNA sequences as input and will compute base pair probability matrices and align the sequences based on their full ensembles of structures. Alternatively, you can also provide base pair probability matrices (dot plots in .ps format) or fixed structures (as annotation in the FASTA alignment) for your sequences. If you provide fixed structures, only those structures and not the entire ensemble of possible structures is aligned. In contrast to LocARNA, CARNA does not pick the most likely consensus structure, but computes the alignment that fits best to all likely structures simultaneously. Hence, CARNA is particularly useful when aligning RNAs like riboswitches, which have more than one stable structure. Also, CARNA is not limited to nested structures, but is able to align arbitrary pseudoknots.
ExpaRNA - 1.0 (2013-01-08)
C++ implementation to find the longest common subsequence of exact pattern matchings (LCS-EPM problem) of two RNAs given with their primary and secondary structure (mfe-structure is used if no structure is available).
Source is available as [tar.gz] as linked above; compiles with Gnu C++ Compiler 4.x.
Copyright by Steffen Heyne, 2008-2013.
If you use ExpaRNA, please cite our article.

To use ExpaRNA, you need the library of the Vienna RNA Package that can be downloaded here.
ExpaRNA compiles also under Cygwin for Windows!
usage example: 'ExpaRNA Examples/HCVirus_IRES_RNAs.fa'
New in 1.0: bugfix, >1000 constraints in output file possible!
INFO-RNA - A Fast Approach to Inverse RNA Folding Satisfying Sequence Constraints
INFO-RNA-2.1.2.tar.gz is available (12-April-2011) [minor bugfix for hairpin loops of size >30bp]
Older source is available as version : 2.1.1, 2.1.0, 2.0, 1.0.

To use INFO-RNA, you need the library of the Vienna RNA Package that can be downloaded here.
Copyright by Anke Busch, 2006-2007.
MARNA source code - enables Multiple Alignment of RNAs with fixed/given structures.
MEMERIS source code
CPSP-tools - Constraint-based Protein Structure Prediction tools CPSP-logo
ELL - Energy Landscape Library ELL-logo
BIU - Bioinformatic Utility Library BIU-logo
LatPack Tools and LatFit
C++ implementation of folding simulations approaches for arbitrary lattice protein models as well as fitting of 3D PDB structures onto lattices.
Copyright by Martin Mann, 2008.
side chain lattice protein fit
RNA Energy Landscape Tools barrier tree
LSSA - Local Sequence Structure Aligment.
C++ implementation for our paper Local Sequence-Structure Motifs in RNA
Please cite this article, if you use the program for a publication.
Source is available as [tar.gz] or [zip]; compiles with Gnu C++ Compiler 3.x.
Copyright Sebastian Will .
CTE-Alignment - Efficient Sequence Alignment with Side Constraints by Cluster Tree Elimination.

Copyright by Sebastian Will.