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Freiburg RNA tools
RNA related tools from the Freiburg Bioinformatics Group
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MoDPepInt Server
Modular domain-peptide interaction tools from the Freiburg Bioinformatics Group
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CPSP web tools
Tools for lattice proteins in the HP-model in various lattice.
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| A variety of different tools that can be installed and used inside the Galaxy. Many tools are already included in the Galaxy Tool Shed. |
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| 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. |
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| 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). |
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| 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. |
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metaMIR - a framework to predict in human interactions between microRNAs (miRNA) and clusters of genes | 
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RNAscClust - RNAscClust - clustering RNA sequences using orthology structure conservation and graph based motifs | |
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SPARSE - A simultaneous alignment and folding tool with quadratic complexity | |
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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. |
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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:
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. |
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CAM - Constraint-based Atom-Atom Mapping |
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ExpaRNA-P - Simultaneous Exact Pattern Matching and Folding of RNAs | |
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GraphProt - modeling binding preferences of RNA-binding proteins | |
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GraphClust - Large Scale structural clustering of RNA sequences (download). | |
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LocalFold - Local Folding of RNA source code distribution | |
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CopraRNA source code bundle for local installation: |
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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.
conda install intarna
See |
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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.
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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.
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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! |
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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. |
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MARNA source code - enables Multiple Alignment of RNAs with fixed/given structures. | |
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MEMERIS source code | |
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CPSP-tools - Constraint-based Protein Structure Prediction tools |
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ELL - Energy Landscape Library |
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BIU - Bioinformatic Utility Library |
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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. |
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RNA Energy Landscape Tools |
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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 . |
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CTE-Alignment - Efficient Sequence Alignment with Side Constraints by Cluster Tree Elimination.
Copyright by Sebastian Will. |
