ArticleBioinformatics (Oxford, England)2009
A partition function algorithm for interacting nucleic acid strands.
Article in Bioinformatics (Oxford, England), 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- Prediction of RNA Joint Secondary Structures Based on Integer Programming.Methods in molecular biology (Clifton, N.J.) · 2026Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- Impact of MICA 3'UTR allelic variability on miRNA binding prediction, a bioinformatic approach.Frontiers in genetics · 2023Article
- LinearPartition: linear-time approximation of RNA folding partition function and base-pairing probabilities.Bioinformatics (Oxford, England) · 2020Article
- A domain-level DNA strand displacement reaction enumerator allowing arbitrary non-pseudoknotted secondary structures.Journal of the Royal Society, Interface · 2020Article
- AptaBlocks: Designing RNA complexes and accelerating RNA-based drug delivery systems.Nucleic acids research · 2018Article
- MechRNA: prediction of lncRNA mechanisms from RNA-RNA and RNA-protein interactions.Bioinformatics (Oxford, England) · 2018Article
- Improving RNA nearest neighbor parameters for helices by going beyond the two-state model.Nucleic acids research · 2018Article
- Structure and Interaction Prediction in Prokaryotic RNA Biology.Microbiology spectrum · 2018Review
- Design of Artificial Riboswitches as Biosensors.Sensors (Basel, Switzerland) · 2017Review
- Optimization of a novel biophysical model using large scale in vivo antisense hybridization data displays improved prediction capabilities of structurally accessible RNA regions.Nucleic acids research · 2017Article
- A comprehensive benchmark of RNA-RNA interaction prediction tools for all domains of life.Bioinformatics (Oxford, England) · 2017Article
- A comprehensive comparison of general RNA-RNA interaction prediction methods.Nucleic acids research · 2016Article
- A Method to Predict the Structure and Stability of RNA/RNA Complexes.Methods in molecular biology (Clifton, N.J.) · 2016Article
- Predicting structure and stability for RNA complexes with intermolecular loop-loop base-pairing.RNA (New York, N.Y.) · 2014Article
- Bioinformatics of prokaryotic RNAs.RNA biology · 2014Review
- The RNA Newton polytope and learnability of energy parameters.Bioinformatics (Oxford, England) · 2013Article
- Full design automation of multi-state RNA devices to program gene expression using energy-based optimization.PLoS computational biology · 2013Article
- Predicting sRNAs and their targets in bacteria.Genomics, proteomics & bioinformatics · 2012Review
- Accessibility and conservation: general features of bacterial small RNA-mRNA interactions?RNA biology · 2012Article
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4 authors.
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Abstract
unlabelledRecent interests, such as RNA interference and antisense RNA regulation, strongly motivate the problem of predicting whether two nucleic acid strands interact. MOTIVATION: Regulatory non-coding RNAs (ncRNAs) such as microRNAs play an important role in gene regulation. Studies on both prokaryotic and eukaryotic cells show that such ncRNAs usually bind to their target mRNA to regulate the translation of corresponding genes. The specificity of these interactions depends on the stability of intermolecular and intramolecular base pairing. While methods like deep sequencing allow to discover an ever increasing set of ncRNAs, there are no high-throughput methods available to detect their associated targets. Hence, there is an increasing need for precise computational target prediction. In order to predict base-pairing probability of any two bases in interacting nucleic acids, it is necessary to compute the interaction partition function over the whole ensemble. The partition function is a scalar value from which various thermodynamic quantities can be derived. For example, the equilibrium concentration of each complex nucleic acid species and also the melting temperature of interacting nucleic acids can be calculated based on the partition function of the complex.
resultsWe present a model for analyzing the thermodynamics of two interacting nucleic acid strands considering the most general type of interactions studied in the literature. We also present a corresponding dynamic programming algorithm that computes the partition function over (almost) all physically possible joint secondary structures formed by two interacting nucleic acids in O(n(6)) time. We verify the predictive power of our algorithm by computing (i) the melting temperature for interacting RNA pairs studied in the literature and (ii) the equilibrium concentration for several variants of the OxyS-fhlA complex. In both experiments, our algorithm shows high accuracy and outperforms competitors. AVAILABILITY: Software and web server is available at http://compbio.cs.sfu.ca/taverna/pirna/. SUPPLEMENTARY INFORMATION: Supplementary data are avaliable at Bioinformatics online.
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