Leipzig – Vienna RNA Package and Toolbox
The ViennaRNA Package is a comprehensive suite of tools and libraries developed by the Institute for Theoretical Chemistry at the University of Vienna, designed for the prediction and analysis of RNA secondary structures. It has become an essential resource in RNA bioinformatics, offering a range of functionalities to support researchers in understanding RNA folding and interactions.
Key Tools and Their Benefits:
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RNAfold: Predicts the minimum free energy (MFE) secondary structure and computes the partition function for single-stranded RNA or DNA sequences. This tool provides insights into RNA folding dynamics and stability.
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RNAalifold: Calculates consensus secondary structures for a set of aligned RNA sequences by combining thermodynamic stability and covariation information, aiding in the study of conserved structural motifs across different species.
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RNAup: Analyzes the thermodynamics of RNA-RNA interactions by calculating the binding probabilities and interaction energies, focusing on the accessibility of binding sites. This is particularly useful for understanding the initial steps of interaction between RNA molecules.
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forna: An interactive tool for RNA secondary structure visualization, allowing users to display and edit structures with ease. It provides an intuitive interface to explore complex RNA structures.
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RNAz: Detects thermodynamically stable and evolutionarily conserved RNA secondary structures in multiple sequence alignments, facilitating the identification of functional RNA elements.
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Bcheck: A wrapper tool for rnpB gene prediction that combines the speed of the rnabob descriptor model with the sensitivity of the infernal covariance model, enhancing the accuracy of gene predictions.
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TSSAR: A web service for predicting bacterial transcription start sites from dRNA-seq data, assisting researchers in annotating transcriptional landscapes.
By offering these robust and versatile tools, the ViennaRNA Package empowers researchers to conduct in-depth RNA analyses, facilitating advancements in understanding RNA structure and function.
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