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Article Dans Une Revue RNA Biology Année : 2015

An assessment of bacterial small RNA target prediction programs.

Résumé

Most bacterial regulatory RNAs exert their function through base-pairing with target RNAs. Computational prediction of targets is a busy research field that offers biologists a variety of web sites and software. However, it is difficult for a non-expert to evaluate how reliable those programs are. Here, we provide a simple benchmark for bacterial sRNA target prediction based on trusted E. coli sRNA/target pairs. We use this benchmark to assess the most recent RNA target predictors as well as earlier programs for RNA-RNA hybrid prediction. Moreover, we consider how the definition of mRNA boundaries can impact overall predictions. Recent algorithms that exploit both conservation of targets and accessibility information offer improved accuracy over previous software. However, even with the best predictors, the number of true biological targets with low scores and non-targets with high scores remains puzzling.

Dates et versions

hal-01464814 , version 1 (10-02-2017)

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Citer

Adrien Pain, Alban Ott, Hamza Amine, Tatiana Rochat, Philippe Bouloc, et al.. An assessment of bacterial small RNA target prediction programs.. RNA Biology, 2015, 12 (5), pp.509-13. ⟨10.1080/15476286.2015.1020269⟩. ⟨hal-01464814⟩
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