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Nat Commun. 2017 Aug 24;8(1):330. doi: 10.1038/s41467-017-00403-z.

On the performance of pre-microRNA detection algorithms.

Author information

1
Molecular Biology and Genetics, Izmir Institute of Technology, Urla, Izmir, 35430, Turkey.
2
Computational Systems Biology, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany. jbaumbac@imada.sdu.dk.
3
Computational Biology, University of Southern Denmark, DK-5230, Odense M, Denmark. jbaumbac@imada.sdu.dk.
4
Bionia Incorporated, IZTEKGEB A8, Urla, Izmir, 35430, Turkey.

Abstract

MicroRNAs are crucial for post-transcriptional gene regulation, and their dysregulation has been associated with diseases like cancer and, therefore, their analysis has become popular. The experimental discovery of miRNAs is cumbersome and, thus, many computational tools have been proposed. Here we assess 13 ab initio pre-miRNA detection approaches using all relevant, published, and novel data sets while judging algorithm performance based on ten intrinsic performance measures. We present an extensible framework, izMiR, which allows for the unbiased comparison of existing algorithms, adding new ones, and combining multiple approaches into ensemble methods. In an exhaustive attempt, we condense the results of millions of computations and show that no method is clearly superior; however, we provide a guideline for biomedical researchers to select a tool. Finally, we demonstrate that combining all of the methods into one ensemble approach, for the first time, allows reliable purely computational pre-miRNA detection in large eukaryotic genomes.As the experimental discovery of microRNAs (miRNAs) is cumbersome, computational tools have been developed for the prediction of pre-miRNAs. Here the authors develop a framework to assess the performance of existing and novel pre-miRNA prediction tools and provide guidelines for selecting an appropriate approach for a given data set.

PMID:
28839141
PMCID:
PMC5571158
DOI:
10.1038/s41467-017-00403-z
[Indexed for MEDLINE]
Free PMC Article

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