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Brief Bioinform. 2017 Mar 1;18(2):306-311. doi: 10.1093/bib/bbw022.

The BRaliBase dent-a tale of benchmark design and interpretation.

Author information

1
Division of Cardiology, University of Nebraska Medical Center, USA.
2
Department of Mathematics, Simon Fraser University, Burnaby, BC, Canada.
3
LIX, CNRS/Inria AMIB, Ecole Polytechnique, Palaiseau, France.
4
Institute for Bioinformatics, Bielefeld University, Bielefeld, Germany.

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.

KEYWORDS:

RNA family database; RNA structural alignment; benchmark

PMID:
26984616
PMCID:
PMC5444242
DOI:
10.1093/bib/bbw022
[Indexed for MEDLINE]
Free PMC Article

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