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RNA Biol. 2015;12(5):509-13. doi: 10.1080/15476286.2015.1020269.

An assessment of bacterial small RNA target prediction programs.

Author information

1
a Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS ; Université Paris-Sud ; Orsay Cedex , France.

Abstract

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.

KEYWORDS:

bacteria; sRNA; sRNA target prediction

PMID:
25760244
PMCID:
PMC4615726
DOI:
10.1080/15476286.2015.1020269
[Indexed for MEDLINE]
Free PMC Article

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