ArticleBioinformatics (Oxford, England)2013
A weighted sampling algorithm for the design of RNA sequences with targeted secondary structure and nucleotide distribution.
Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- RNA design: update on computational frameworks and programs for inverse RNA folding.Briefings in bioinformatics · 2026Review
- RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs.Algorithms for molecular biology : AMB · 2025Article
- RNA Design Using incaRNAfbinv Demonstrated with the Identification of Functional RNA Motifs in Hepatitis Delta Virus.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Predicting RNA sequence-structure likelihood via structure-aware deep learning.BMC bioinformatics · 2024Article
- Infrared: a declarative tree decomposition-powered framework for bioinformatics.Algorithms for molecular biology : AMB · 2024Article
- Developing Complex RNA Design Applications in the Infrared Framework.Methods in molecular biology (Clifton, N.J.) · 2024Article
- RNA design via structure-aware multifrontier ensemble optimization.Bioinformatics (Oxford, England) · 2023Article
- Fitness functions for RNA structure design.Nucleic acids research · 2023Article
- The energy-spectrum of bicompatible sequences.Algorithms for molecular biology : AMB · 2021Article
- ENTRNA: a framework to predict RNA foldability.BMC bioinformatics · 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
- RNA inverse folding using Monte Carlo tree search.BMC bioinformatics · 2017Article
- RNAblueprint: flexible multiple target nucleic acid sequence design.Bioinformatics (Oxford, England) · 2017Article
- Article
- RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory.BMC bioinformatics · 2016Article
- 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
- antaRNA: ant colony-based RNA sequence design.Bioinformatics (Oxford, England) · 2015Article
- Multi-objective optimization for RNA design with multiple target secondary structures.BMC bioinformatics · 2015Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationsThe design of RNA sequences folding into predefined secondary structures is a milestone for many synthetic biology and gene therapy studies. Most of the current software uses similar local search strategies (i.e. a random seed is progressively adapted to acquire the desired folding properties) and more importantly do not allow the user to control explicitly the nucleotide distribution such as the GC-content in their sequences. However, the latter is an important criterion for large-scale applications as it could presumably be used to design sequences with better transcription rates and/or structural plasticity.
resultsIn this article, we introduce IncaRNAtion, a novel algorithm to design RNA sequences folding into target secondary structures with a predefined nucleotide distribution. IncaRNAtion uses a global sampling approach and weighted sampling techniques. We show that our approach is fast (i.e. running time comparable or better than local search methods), seedless (we remove the bias of the seed in local search heuristics) and successfully generates high-quality sequences (i.e. thermodynamically stable) for any GC-content. To complete this study, we develop a hybrid method combining our global sampling approach with local search strategies. Remarkably, our glocal methodology overcomes both local and global approaches for sampling sequences with a specific GC-content and target structure. AVAILABILITY: IncaRNAtion is available at csb.cs.mcgill.ca/incarnation/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.