ArticleBriefings in bioinformatics2017
The BRaliBase dent-a tale of benchmark design and interpretation.
Article in Briefings in bioinformatics, 2017. 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.
- DEBFold: Computational Identification of RNA Secondary Structures for Sequences across Structural Families Using Deep Learning.Journal of chemical information and modeling · 2024Article
- LaRA 2: parallel and vectorized program for sequence-structure alignment of RNA sequences.BMC bioinformatics · 2022Article
- Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs with Markov chains.Algorithms for molecular biology : AMB · 2020Article
- RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency.RNA (New York, N.Y.) · 2020Article
- Essential guidelines for computational method benchmarking.Genome biology · 2019Review
- Freiburg RNA tools: a central online resource for RNA-focused research and teaching.Nucleic acids research · 2018Article
- TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.Nucleic acids research · 2017Article
Corrections and comments
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Authors and funding
4 authors.
Funding
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Abstract
BRaliBase is a widely used benchmark for assessing the accuracy of RNA secondary structure alignment methods. In most case studies based on the BRaliBase benchmark, one can observe a puzzling drop in accuracy in the 40-60% sequence identity range, the so-called 'BRaliBase Dent'. In this article, we show this dent is owing to a bias in the composition of the BRaliBase benchmark, namely the inclusion of a disproportionate number of transfer RNAs, which exhibit a conserved secondary structure. Our analysis, aside of its interest regarding the specific case of the BRaliBase benchmark, also raises important questions regarding the design and use of benchmarks in computational biology.
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