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)
• LocARNA Global and local alignment of RNAs (» download) (» movie)
• Carna
Alignment of structure ensembles
• ExpaRNA Exact matching of sequence-structure motives (» download) (» movie)
• IntaRNA RNA-RNA interaction prediction (» download) (» movie)
• INFO-RNA Inverse folding of RNA /
Sequence Design
(» download)
• MARNA Fixed structure alignment (» download)
RNA motif

Multiple Alignment of RNAs
MoDPepInt Server
Modular domain-peptide interaction tools from the Freiburg Bioinformatics Group
• SH2PepInt
SH2-peptide interaction prediction New!
• SH3PepInt
SH3-peptide interaction prediction New!
• PDZPepInt
PDZ-peptide interaction prediction New!
CPSP web tools
Tools for lattice proteins in the HP-model in various lattice.
• HPstruct Optimal structure prediction (» download)
• HPview Structure visualization (» download)
• HPdeg Degeneracy calculation (» download)
• HPnnet Neutral network expansion (» download)
• HPdesign Sequence design (inverse folding) (» download)
• LatFit Lattice models of PDB structures (» download)
FCC-HP protein
SECISDesign - A Server to Design SECIS-Elements within the Coding Sequence

Software and Libraries for Download

SPARSE - A simultaneous alignment and folding tool with quadratic complexity
antaRNA - Ant Colony Optimized RNA Sequence Design
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 - 1.2.5 (2011-06-10) - Efficient target prediction incorporating accessibility of interaction sites.
IntaRNA requires the library of the Vienna RNA Package (only versions 1.8.2 - 1.8.5 are supported). The Vienna RNA Package in version 1.8.5 is provided here.
If you use IntaRNA, please cite our article.
Copyright by Anke Busch and Andreas S. Richter, 2008-2011.
LocARNA - Global and Local Alignment of RNA.
A tool for pairwise and multiple, global and local alignment of RNA with simultaneous folding.
Copyright by Sebastian Will, 2006-2009.
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
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.