ArticleRNA (New York, N.Y.)2012
Abstract folding space analysis based on helices.
Article in RNA (New York, N.Y.), 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 15 citations in OpenAlex.
- Classified Dynamic Programming in RNA Structure Analysis.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Simulation of Folding Kinetics for Aligned RNAs.Genes · 2021Article
- Helix-Based RNA Landscape Partition and Alternative Secondary Structure Determination.ACS omega · 2019Article
- Towards an understanding of RNA structural modalities: a riboswitch case study.Computational and mathematical biophysics · 2019Article
- Swellix: a computational tool to explore RNA conformational space.BMC bioinformatics · 2017Article
- New insights from cluster analysis methods for RNA secondary structure prediction.Wiley interdisciplinary reviews. RNA · 2016Review
- Random versus Deterministic Descent in RNA Energy Landscape Analysis.Advances in bioinformatics · 2016Article
- An implementation of the Gillespie algorithm for RNA kinetics with logarithmic time update.Nucleic acids research · 2015Article
- Thermodynamic matchers for the construction of the cuckoo RNA family.RNA biology · 2015Article
- Profiling small RNA reveals multimodal substructural signals in a Boltzmann ensemble.Nucleic acids research · 2014Article
- Analysing RNA-kinetics based on folding space abstraction.BMC bioinformatics · 2014Article
- Adaptation and modification of three CRISPR loci in two closely related cyanobacteria.RNA biology · 2013Article
- Bellman's GAP--a language and compiler for dynamic programming in sequence analysis.Bioinformatics (Oxford, England) · 2013Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
RNA has many pivotal functions especially in the regulation of gene expression by ncRNAs. Identification of their structure is an important requirement for understanding their function. Structure prediction alone is often insufficient for this task, due to algorithmic problems, parameter inaccuracies, and biological peculiarities. Among the latter, there are base modifications, cotranscriptional folding leading to folding traps, and conformational switching as in the case of riboswitches. All these require more in-depth analysis of the folding space. The major drawback, which all methods have to cope with, is the exponential growth of the folding space. Therefore, methods are often limited in the sequence length they can analyze, or they make use of heuristics, sampling, or abstraction. Our approach adopts the abstraction strategy and remedies some problems of existing methods. We introduce a position-specific abstraction based on helices that we term helix index shapes, or hishapes for short. Utilizing a dynamic programming framework, we have implemented this abstraction in the program RNAHeliCes. Furthermore, we developed two hishape-based methods, one for energy barrier estimation, called HiPath, and one for abstract structure comparison, termed HiTed. We demonstrate the superior performance of HiPath compared to other existing methods and the competitive accuracy of HiTed. RNAHeliCes, together with HiPath and HiTed, are available for download at http://www.cyanolab.de/software/RNAHeliCes.htm.
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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.