The BRaliBase dent-a tale of benchmark design and interpretation.
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ABSTRACT:
SUBMITTER: Lowes B
PROVIDER: S-EPMC5444242 | biostudies-literature | 2017 Mar
REPOSITORIES: biostudies-literature
Publications
The BRaliBase dent-a tale of benchmark design and interpretation.
Löwes Benedikt B Chauve Cedric C Ponty Yann Y Giegerich Robert R
Briefings in bioinformatics 20170301 2
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 ...[more]
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