ArticleBioinformatics (Oxford, England)2015
antaRNA: ant colony-based RNA sequence design.
Article in Bioinformatics (Oxford, England), 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- RNA design: update on computational frameworks and programs for inverse RNA folding.Briefings in bioinformatics · 2026Review
- Factorization machine with quadratic-optimization annealing for RNA inverse folding and evaluation of binary-integer encoding and nucleotide assignment.Scientific reports · 2026Article
- RNA inverse folding can be solved in linear time for structures without isolated stacks or base pairs.Algorithms for molecular biology : AMB · 2025Article
- DRAG: design RNAs as hierarchical graphs with reinforcement learning.Briefings in bioinformatics · 2025Article
- Secondary-Structure-Informed RNA Inverse Design via Relational Graph Neural Networks.Non-coding RNA · 2025Article
- DesiRNA: structure-based design of RNA sequences with a replica exchange Monte Carlo approach.Nucleic acids research · 2025Article
- Toward Increasing the Credibility of RNA Design.Methods in molecular biology (Clifton, N.J.) · 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
- RNAelem: an algorithm for discovering sequence-structure motifs in RNA bound by RNA-binding proteins.Bioinformatics advances · 2024Article
- RNA design via structure-aware multifrontier ensemble optimization.Bioinformatics (Oxford, England) · 2023Article
- Fitness functions for RNA structure design.Nucleic acids research · 2023Article
- aRNAque: an evolutionary algorithm for inverse pseudoknotted RNA folding inspired by Lévy flights.BMC bioinformatics · 2022Article
- MoiRNAiFold: a novel tool for complex in silico RNA design.Nucleic acids research · 2021Article
- High-throughput interrogation of programmed ribosomal frameshifting in human cells.Nature communications · 2020Article
- ENTRNA: a framework to predict RNA foldability.BMC bioinformatics · 2019Article
- Design of highly active double-pseudoknotted ribozymes: a combined computational and experimental study.Nucleic acids research · 2019Article
- Metabolic pathways synthesis based on ant colony optimization.Scientific reports · 2018Article
- Distinctive features of lincRNA gene expression suggest widespread RNA-independent functions.Life science alliance · 2018Article
- Freiburg RNA tools: a central online resource for RNA-focused research and teaching.Nucleic acids research · 2018Article
- Design of RNAs: comparing programs for inverse RNA folding.Briefings in bioinformatics · 2018Review
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
motivationRNA sequence design is studied at least as long as the classical folding problem. Although for the latter the functional fold of an RNA molecule is to be found ,: inverse folding tries to identify RNA sequences that fold into a function-specific target structure. In combination with RNA-based biotechnology and synthetic biology ,: reliable RNA sequence design becomes a crucial step to generate novel biochemical components.
resultsIn this article ,: the computational tool antaRNA is presented. It is capable of compiling RNA sequences for a given structure that comply in addition with an adjustable full range objective GC-content distribution ,: specific sequence constraints and additional fuzzy structure constraints. antaRNA applies ant colony optimization meta-heuristics and its superior performance is shown on a biological datasets. AVAILABILITY AND IMPLEMENTATION: http://www.bioinf.uni-freiburg.de/Software/antaRNA CONTACT: backofen@informatik.uni-freiburg.de 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.