The BRaliBase Dent – a Tale of Benchmark Design and Interpretation

Löwes B, Chauve C, Ponty Y, Giegerich R (2017)
Briefings in Bioinformatics 18(2): 306-311.

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Zeitschriftenaufsatz | Veröffentlicht | Englisch
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Abstract / Bemerkung
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 the present note, we show this dent is due to a bias in the composition of the BRaliBase benchmark, namely the inclusion of a disproportionate number of tRNAs, which exhibit a very 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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Zeitschriftentitel
Briefings in Bioinformatics
Band
18
Zeitschriftennummer
2
Seite
306 - 311
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Löwes B, Chauve C, Ponty Y, Giegerich R. The BRaliBase Dent – a Tale of Benchmark Design and Interpretation. Briefings in Bioinformatics. 2017;18(2):306-311.
Löwes, B., Chauve, C., Ponty, Y., & Giegerich, R. (2017). The BRaliBase Dent – a Tale of Benchmark Design and Interpretation. Briefings in Bioinformatics, 18(2), 306-311. doi:10.1093/bib/bbw022
Löwes, B., Chauve, C., Ponty, Y., and Giegerich, R. (2017). The BRaliBase Dent – a Tale of Benchmark Design and Interpretation. Briefings in Bioinformatics 18, 306-311.
Löwes, B., et al., 2017. The BRaliBase Dent – a Tale of Benchmark Design and Interpretation. Briefings in Bioinformatics, 18(2), p 306-311.
B. Löwes, et al., “The BRaliBase Dent – a Tale of Benchmark Design and Interpretation”, Briefings in Bioinformatics, vol. 18, 2017, pp. 306-311.
Löwes, B., Chauve, C., Ponty, Y., Giegerich, R.: The BRaliBase Dent – a Tale of Benchmark Design and Interpretation. Briefings in Bioinformatics. 18, 306-311 (2017).
Löwes, Benedikt, Chauve, Cedric, Ponty, Yann, and Giegerich, Robert. “The BRaliBase Dent – a Tale of Benchmark Design and Interpretation”. Briefings in Bioinformatics 18.2 (2017): 306-311.

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TurboFold II: RNA structural alignment and secondary structure prediction informed by multiple homologs.
Tan Z, Fu Y, Sharma G, Mathews DH., Nucleic Acids Res 45(20), 2017
PMID: 29036420

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