ArticleBMC bioinformatics2011
RNAexinv: An extended inverse RNA folding from shape and physical attributes to sequences.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Partial RNA design.Bioinformatics (Oxford, England) · 2024Article
- RNAincoder: a deep learning-based encoder for RNA and RNA-associated interaction.Nucleic acids research · 2023Article
- A pipeline for computational design of novel RNA-like topologies.Nucleic acids research · 2018Article
- Design of RNAs: comparing programs for inverse RNA folding.Briefings in bioinformatics · 2018Review
- RNA inverse folding using Monte Carlo tree search.BMC bioinformatics · 2017Article
- incaRNAfbinv: a web server for the fragment-based design of RNA sequences.Nucleic acids research · 2016Article
- An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.Frontiers in genetics · 2016Article
- Article
- ERD: a fast and reliable tool for RNA design including constraints.BMC bioinformatics · 2015Article
- A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.Bioinformatics (Oxford, England) · 2013Article
- mRNA secondary structure optimization using a correlated stem-loop prediction.Nucleic acids research · 2013Article
- Inverse RNA folding solution based on multi-objective genetic algorithm and Gibbs sampling method.EXCLI journal · 2013Article
- A global sampling approach to designing and reengineering RNA secondary structures.Nucleic acids research · 2012Article
- Frnakenstein: multiple target inverse RNA folding.BMC bioinformatics · 2012Article
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3 authors.
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Abstract
backgroundRNAexinv is an interactive java application that performs RNA sequence design, constrained to yield a specific RNA shape and physical attributes. It is an extended inverse RNA folding program with the rationale behind that the generated sequences should not only fold into a desired structure, but they should also exhibit favorable attributes such as thermodynamic stability and mutational robustness. RNAexinv considers not only the secondary structure in order to design sequences, but also the mutational robustness and the minimum free energy. The sequences that are generated may not fully conform with the given RNA secondary structure, but they will strictly conform with the RNA shape of the given secondary structure and thereby take into consideration the recommended values of thermodynamic stability and mutational robustness that are provided.
resultsThe output consists of designed sequences that are generated by the proposed method. Selecting a sequence displays the secondary structure drawings of the target and the predicted fold of the sequence, including some basic information about the desired and achieved thermodynamic stability and mutational robustness. RNAexinv can be used successfully without prior experience, simply specifying an initial RNA secondary structure in dot-bracket notation and numerical values for the desired neutrality and minimum free energy. The package runs under LINUX operating system. Secondary structure predictions are performed using the Vienna RNA package.
conclusionsRNAexinv is a user friendly tool that can be used for RNA sequence design. It is especially useful in cases where a functional stem-loop structure of a natural sequence should be strictly kept in the designed sequences but a distant motif in the rest of the structure may contain one more or less nucleotide at the expense of another, as long as the global shape is preserved. This allows the insertion of physical observables as constraints. RNAexinv is available at http://www.cs.bgu.ac.il/~RNAexinv.
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