Bioinformatics
Institute of Computer Science
University Freiburg
de

Software/Server

Web-Services

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

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

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

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 - 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.