Assessing computational tools for the discovery of small RNA genes in bacteria
- 1Department of Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
- 2Computer Science Department, Wellesley College, Wellesley, Massachusetts 02481, USA
Abstract
Over the past decade, a number of biocomputational tools have been developed to predict small RNA (sRNA) genes in bacterial genomes. In this study, several of the leading biocomputational tools, which use different methodologies, were investigated. The performance of the tools, both individually and in combination, was evaluated on ten sets of benchmark data, including data from a novel RNA-seq experiment conducted in this study. The results of this study offer insight into the utility as well as the limitations of the leading biocomputational tools for sRNA identification and provide practical guidance for users of the tools.
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Footnotes
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↵3 Corresponding author.
E-mail btjaden{at}wellesley.edu.
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Article published online ahead of print. Article and publication date are at http://www.rnajournal.org/cgi/doi/10.1261/rna.2689811.
- Received February 22, 2011.
- Accepted June 10, 2011.
- Copyright © 2011 RNA Society
Freely available online through the RNA Open Access option.