Bioinformatics
Institute of Computer Science
University Freiburg
de

Software/Server

Server and Web-Applications

BioBayesNet - a web server for feature extraction and bayesian network modeling of biological sequence data
CPSP web tools     (New version !)
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 (New!) Lattice models of PDB structures (» download)
FCC-HP protein
Freiburg RNA tools     (New !!!)
RNA related tools from the Freiburg Bioinformatics Group
• ExpaRNA Exact matching of sequence-structure motives (» download) (» movie)
• IntaRNA RNA-RNA interaction prediction (» download) (» movie)
• LocARNA Local sequence-structure alignment of RNAs (» download) (» movie)
RNA motif
INFO-RNA - A Server for Inverse Folding of RNA
MARNA - A Server for Multiple Alignment of RNAs Multiple Alignment of RNAs
SECISDesign - A Server to Design SECIS-Elements within the Coding Sequence
NIPU server - Display splicing regulatory motifs and single-stranded mRNA regions
TassDB - TAndem Splice Site DataBase

Software and Libraries

LocalFold source code
IntaRNA - 1.2.5 (2011-06-10) NEW Version - Efficient Target Prediction Incorporating Accessibility of Target Sites
Default parameters have changed with version 1.2.
To use IntaRNA, you need the library of the Vienna RNA Package (version ≥1.8.2). The latest version of the Vienna RNA Package version can be downloaded here.
If you use our tool for your own scientific publication, 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 - 0.8.3 (2011-02-25)
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] or [zip]; compiles with Gnu C++ Compiler 4.x.
Copyright by Steffen Heyne, 2008-2011.
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 0.8.3: Command line options changed!
New in 0.6: FASTA file input, LocARNA constrained output, removed XERCES-C dependency, code clean-up
INFO-RNA - A Fast Approch 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.