The BRaliBase Dent – a Tale of Benchmark Design and Interpretation

Löwes B, Chauve C, Ponty Y, Giegerich R (2016)
Briefings in Bioinformatics.

Journal Article | Epub ahead of print | English

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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 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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Löwes B, Chauve C, Ponty Y, Giegerich R. The BRaliBase Dent – a Tale of Benchmark Design and Interpretation. Briefings in Bioinformatics. 2016.
Löwes, B., Chauve, C., Ponty, Y., & Giegerich, R. (2016). The BRaliBase Dent – a Tale of Benchmark Design and Interpretation. Briefings in Bioinformatics.
Löwes, B., Chauve, C., Ponty, Y., and Giegerich, R. (2016). The BRaliBase Dent – a Tale of Benchmark Design and Interpretation. Briefings in Bioinformatics.
Löwes, B., et al., 2016. The BRaliBase Dent – a Tale of Benchmark Design and Interpretation. Briefings in Bioinformatics.
B. Löwes, et al., “The BRaliBase Dent – a Tale of Benchmark Design and Interpretation”, Briefings in Bioinformatics, 2016.
Löwes, B., Chauve, C., Ponty, Y., Giegerich, R.: The BRaliBase Dent – a Tale of Benchmark Design and Interpretation. Briefings in Bioinformatics. (2016).
Löwes, Benedikt, Chauve, Cedric, Ponty, Yann, and Giegerich, Robert. “The BRaliBase Dent – a Tale of Benchmark Design and Interpretation”. Briefings in Bioinformatics (2016).
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PMID: 26984616
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