Freiburg RNA Toolbox
The Freiburg RNA Toolbox provides a comprehensive set of online tools for RNA research, covering various aspects such as sequence-structure alignments, clustering, interaction prediction, identification of homologs, sequence design, and more.
Tools
Interaction Prediction
- CopraRNA : A tool for sRNA target prediction that combines whole genome IntaRNA predictions using homologous sRNA sequences from distinct organisms.
- IntaRNA : A tool for predicting RNA-RNA interactions, including mRNA target sites for non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs).
- metaMIR : A framework to predict interactions in human between miRNAs and clusters of genes.
Seq-Str Alignment
- LocARNA : A tool for multiple alignments of RNAs based on their sequence and structure similarity, considering the whole ensemble of secondary structures for each RNA.
- CARNA : A tool for multiple alignment of RNA molecules based on their full ensembles of structures, computing the alignment that fits best to all likely structures simultaneously.
- MARNA : A tool for multiple sequence-structure alignments considering a single fixed structure for each sequence only.
- ExpaRNA : A fast, motif-based comparison and alignment tool for RNA molecules.
CRISPR
- CRISPRmap : A tool providing a quick and detailed insight into repeat conservation and diversity of both bacterial and archaeal systems.
- CRISPRloci : A full suite for CRISPR locus characterization that includes CRISPR array orientation, detection of conserved leaders, cas gene annotation, and subtype classification.
Sequence Design
- AntaRNA : An Ant-Colony Optimization based tool solving the RNA inverse folding problem, designing RNA sequences satisfying a set of constraints.
- INFORNA : A server for the design of RNA sequences that fold into a given pseudo-knot free RNA secondary structure.
- SECISDesign : A server for the design of SECIS-elements within the coding sequence of an mRNA with both structure and sequence constraints.
Splicing
- NIPU : A tool allowing to display splicing regulatory motifs and single-stranded regions.
SNP & Mutation
- CopomuS : A tool rating and ranking possible compensatory mutations of IntaRNA predictions.
- MutaRNA : A tool predicting and visualizing the mutation-induced structure changes of a single-nucleotide polymorphism (SNP) in an RNA sequence.
- RaSE : An offline tool using the graph vectorization technique to compute a score indicative of the structural stability responsibility of each nucleotide in an RNA sequence.
Classification
- BrainDead : A tool learning a two-class model for short RNA sequences based on accessibility-enhanced k-mer features and applying it for class prediction of unknown RNAs.
Gene set extension
- DiGI : A tool predicting and ranking a list of unknown genes based on their probabilities to be related to a given genetic disease.
Additional Resources
The Freiburg Bioinformatics Group also provides:
- MoDPepInt Server : A simple and interactive webserver for predicting the binding partners of three different modular protein domains.
- CPSP-Tools Server : An exact and efficient approach to identify optimal structures of lattice proteins within the hydrophobic-polar (HP) model.
- Galaxy Project - Uni Freiburg : A framework for scientists on e.g. NGS data analyses, genome annotation analyses, proteomics, and metabolomics analysis.
- CMV server : Tools for the visualization of RNA family models, also known as co-variance models (CM) and Hidden Markov Models (HMM).
Find this service in BioTools here.
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