ArticleNucleic acids research2012
A global sampling approach to designing and reengineering RNA secondary structures.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Simulated Annealing for RNA Design with SIMARD.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Mitochondrial sequencing identifies long noncoding RNA features that promote binding to PNPase.American journal of physiology. Cell physiology · 2024Article
- Fitness functions for RNA structure design.Nucleic acids research · 2023Article
- The energy-spectrum of bicompatible sequences.Algorithms for molecular biology : AMB · 2021Article
- On the emergence of structural complexity in RNA replicators.RNA (New York, N.Y.) · 2019Article
- Genetic robustness of let-7 miRNA sequence-structure pairs.RNA (New York, N.Y.) · 2019Article
- Fixed-parameter tractable sampling for RNA design with multiple target structures.BMC bioinformatics · 2019Article
- Design of RNAs: comparing programs for inverse RNA folding.Briefings in bioinformatics · 2018Review
- An Adaptive Defect Weighted Sampling Algorithm to Design Pseudoknotted RNA Secondary Structures.Frontiers in genetics · 2016Article
- Using structural and evolutionary information to detect and correct pyrosequencing errors in noncoding RNAs.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.Bioinformatics (Oxford, England) · 2013Article
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Authors and funding
7 authors.
Funding
Abstract
The development of algorithms for designing artificial RNA sequences that fold into specific secondary structures has many potential biomedical and synthetic biology applications. To date, this problem remains computationally difficult, and current strategies to address it resort to heuristics and stochastic search techniques. The most popular methods consist of two steps: First a random seed sequence is generated; next, this seed is progressively modified (i.e. mutated) to adopt the desired folding properties. Although computationally inexpensive, this approach raises several questions such as (i) the influence of the seed; and (ii) the efficiency of single-path directed searches that may be affected by energy barriers in the mutational landscape. In this article, we present RNA-ensign, a novel paradigm for RNA design. Instead of taking a progressive adaptive walk driven by local search criteria, we use an efficient global sampling algorithm to examine large regions of the mutational landscape under structural and thermodynamical constraints until a solution is found. When considering the influence of the seeds and the target secondary structures, our results show that, compared to single-path directed searches, our approach is more robust, succeeds more often and generates more thermodynamically stable sequences. An ensemble approach to RNA design is thus well worth pursuing as a complement to existing approaches. RNA-ensign is available at http://csb.cs.mcgill.ca/RNAensign.
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