Software/Server
RNA-related tools from the Freiburg Bioinformatics Group
| Tool | Description | |
|---|---|---|
| CRISPRmap | 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 | Download | New! |
| LocARNA | Global and local alignment of RNAs | Download | Movie |
| CARNA | Alignment of structure ensembles | Download |
| MARNA | Fixed structure alignment | Download |
| ExpaRNA | Exact matching of sequence-structure motifs | Download | Movie |
| INFO-RNA | Inverse folding of RNA / Sequence Design | Download |
| SECISDesign | Insert SECIS-elements in coding mRNAs | |
| NIPU | Splicing of regular motifs | |
| RaSE | Structural stability estimator of RNA nucleotides |
Modular domain-peptide interaction tools from the Freiburg Bioinformatics Group
A collection of tools and resources developed for the Galaxy platform by the Freiburg Galaxy Project.
A variety of different tools that can be installed and used inside Galaxy. Many tools are already included in the Galaxy Tool Shed.
An easily distributable full-fledged Galaxy installation for testing, teaching, and presenting new tools and features.
A Galaxy Docker instance specifically set up for high-throughput RNA analyses. Developed by the RNA Bioinformatics Center, part of the German Network for Bioinformatics Infrastructure (de.NBI).
Integrates IPython Notebook, an interactive computational environment, with Galaxy. Aims to unlock creativity in data analysis and enhance training courses. Watch the Galaxy IPython Video to learn more.
metaMIR is a framework to predict in human interactions between microRNAs (miRNA) and clusters of genes. The user provides a set of genes to be targeted, and optionally genes not to be targeted. The analysis is performed to identify miRNAs that may simultaneously interact with a number of genes.
For further details, recent releases etc. see metaMIR @ github.
In order to use metaMIR you can:
RNAscClust - clustering RNA sequences using orthology structure conservation and graph based motifs
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:
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
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
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 Bioconda using:
conda install intarna
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 RNAs 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 provided 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 versions: 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.
ELL - Energy Landscape Library.
BIU - Bioinformatic Utility Library.
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.
LSSA - Local Sequence Structure Alignment.
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.
