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.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
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DOI
Autor*in
Löwes, BenediktUniBi; Chauve, Cedric; Ponty, Yann; Giegerich, RobertUniBi
Einrichtung
Centrum für Biotechnologie > Graduate Center
Technische Fakultät > Int. Graduiertenkolleg DiDy (GRK 1906)
Technische Fakultät > AG Praktische Informatik
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.
Stichworte
RNA structural alignment; benchmark; RNA family database
Erscheinungsjahr
2017
Zeitschriftentitel
Briefings in Bioinformatics
Band
18
Ausgabe
2
Seite(n)
306 - 311
ISSN
1467-5463
Page URI
https://pub.uni-bielefeld.de/record/2901460

Zitieren

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, Benedikt, Chauve, Cedric, Ponty, Yann, and Giegerich, Robert. 2017. “The BRaliBase Dent – a Tale of Benchmark Design and Interpretation”. Briefings in Bioinformatics 18 (2): 306-311.
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.

3 Zitationen in Europe PMC

Daten bereitgestellt von Europe PubMed Central.

Essential guidelines for computational method benchmarking.
Weber LM, Saelens W, Cannoodt R, Soneson C, Hapfelmeier A, Gardner PP, Boulesteix AL, Saeys Y, Robinson MD., Genome Biol 20(1), 2019
PMID: 31221194
Freiburg RNA tools: a central online resource for RNA-focused research and teaching.
Raden M, Ali SM, Alkhnbashi OS, Busch A, Costa F, Davis JA, Eggenhofer F, Gelhausen R, Georg J, Heyne S, Hiller M, Kundu K, Kleinkauf R, Lott SC, Mohamed MM, Mattheis A, Miladi M, Richter AS, Will S, Wolff J, Wright PR, Backofen R., Nucleic Acids Res 46(w1), 2018
PMID: 29788132
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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