ReviewWiley interdisciplinary reviews. RNA2016
New insights from cluster analysis methods for RNA secondary structure prediction.
Review in Wiley interdisciplinary reviews. RNA, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Can geometric combinatorics improve RNA branching predictions?BMC bioinformatics · 2025Article
- Helix-Based RNA Landscape Partition and Alternative Secondary Structure Determination.ACS omega · 2019Article
- Analyzing Secondary Structure Patterns in DNA Aptamers Identified via CompELS.Molecules (Basel, Switzerland) · 2019Article
- PATTERNA: transcriptome-wide search for functional RNA elements via structural data signatures.Genome biology · 2018Article
- Statistical modeling of RNA structure profiling experiments enables parsimonious reconstruction of structure landscapes.Nature communications · 2018Article
- Opportunities and Challenges in RNA Structural Modeling and Design.Biophysical journal · 2017Article
- Comparative and integrative analysis of RNA structural profiling data: current practices and emerging questions.Quantitative biology (Beijing, China) · 2017Article
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Abstract
A widening gap exists between the best practices for RNA secondary structure prediction developed by computational researchers and the methods used in practice by experimentalists. Minimum free energy predictions, although broadly used, are outperformed by methods which sample from the Boltzmann distribution and data mine the results. In particular, moving beyond the single structure prediction paradigm yields substantial gains in accuracy. Furthermore, the largest improvements in accuracy and precision come from viewing secondary structures not at the base pair level but at lower granularity/higher abstraction. This suggests that random errors affecting precision and systematic ones affecting accuracy are both reduced by this 'fuzzier' view of secondary structures. Thus experimentalists who are willing to adopt a more rigorous, multilayered approach to secondary structure prediction by iterating through these levels of granularity will be much better able to capture fundamental aspects of RNA base pairing. WIREs RNA 2016, 7:278-294. doi: 10.1002/wrna.1334 For further resources related to this article, please visit the WIREs website.
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