ArticleNucleic acids research2013
CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 59 papers.
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Who cites it
59 citing papers in PubMed, 123 citations in OpenAlex.
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- Nucleotide dependency analysis of genomic language models detects functional elements.Nature genetics · 2025Article
- RiNALMo: general-purpose RNA language models can generalize well on structure prediction tasks.Nature communications · 2025Article
- DesiRNA: structure-based design of RNA sequences with a replica exchange Monte Carlo approach.Nucleic acids research · 2025Article
- A Hitchhiker's guide to RNA-RNA structure and interaction prediction tools.Briefings in bioinformatics · 2023Review
- Machine learning for RNA 2D structure prediction benchmarked on experimental data.Briefings in bioinformatics · 2023Review
- Rtools: A Web Server for Various Secondary Structural Analyses on Single RNA Sequences.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Persistent Homology for RNA Data Analysis.Methods in molecular biology (Clifton, N.J.) · 2023Article
- RNA secondary structure packages evaluated and improved by high-throughput experiments.Nature methods · 2022Article
- Advances and opportunities in RNA structure experimental determination and computational modeling.Nature methods · 2022Review
- KnotAli: informed energy minimization through the use of evolutionary information.BMC bioinformatics · 2022Article
- LinAliFold and CentroidLinAliFold: fast RNA consensus secondary structure prediction for aligned sequences using beam search methods.Bioinformatics advances · 2022Article
- Review
- Learning the Fastest RNA Folding Path Based on Reinforcement Learning and Monte Carlo Tree Search.Molecules (Basel, Switzerland) · 2021Article
- Article
- Rfam 14: expanded coverage of metagenomic, viral and microRNA families.Nucleic acids research · 2021Article
- aliFreeFoldMulti: alignment-free method to predict secondary structures of multiple RNA homologs.NAR genomics and bioinformatics · 2020Article
- The locality dilemma of Sankoff-like RNA alignments.Bioinformatics (Oxford, England) · 2020Article
- RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency.RNA (New York, N.Y.) · 2020Article
Corrections and comments
- Erratum issued
Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server. As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank. We also provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks on both data sets offer insight into the relative performance of RNA secondary structure prediction methods on RNAs of different size and with respect to different types of structure. According to our tests, on the average, the most accurate predictions obtained by a comparative approach are generated by CentroidAlifold, MXScarna, RNAalifold and TurboFold. On the average, the most accurate predictions obtained by single-sequence analyses are generated by CentroidFold, ContextFold and IPknot. The best comparative methods typically outperform the best single-sequence methods if an alignment of homologous RNA sequences is available. This article presents the results of our benchmarks as of 3 October 2012, whereas the rankings presented online are continuously updated. We will gladly include new prediction methods and new measures of accuracy in the new editions of CompaRNA benchmarks.
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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.