Open Access Highly Accessed Methodology article

Non-coding RNA detection methods combined to improve usability, reproducibility and precision

Peter Raasch1, Ulf Schmitz1, Nadja Patenge2, Julio Vera1, Bernd Kreikemeyer2 and Olaf Wolkenhauer1*

Author Affiliations

1 Systems Biology and Bioinformatics Group, University of Rostock, D-18057 Rostock, Germany

2 Department of Medical Microbiology, Virology and Hygiene, University Hospital Rostock, Schillingallee 70, D-18055 Rostock, Germany

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BMC Bioinformatics 2010, 11:491  doi:10.1186/1471-2105-11-491

Published: 29 September 2010



Non-coding RNAs gain more attention as their diverse roles in many cellular processes are discovered. At the same time, the need for efficient computational prediction of ncRNAs increases with the pace of sequencing technology. Existing tools are based on various approaches and techniques, but none of them provides a reliable ncRNA detector yet. Consequently, a natural approach is to combine existing tools. Due to a lack of standard input and output formats combination and comparison of existing tools is difficult. Also, for genomic scans they often need to be incorporated in detection workflows using custom scripts, which decreases transparency and reproducibility.


We developed a Java-based framework to integrate existing tools and methods for ncRNA detection. This framework enables users to construct transparent detection workflows and to combine and compare different methods efficiently. We demonstrate the effectiveness of combining detection methods in case studies with the small genomes of Escherichia coli, Listeria monocytogenes and Streptococcus pyogenes. With the combined method, we gained 10% to 20% precision for sensitivities from 30% to 80%. Further, we investigated Streptococcus pyogenes for novel ncRNAs. Using multiple methods--integrated by our framework--we determined four highly probable candidates. We verified all four candidates experimentally using RT-PCR.


We have created an extensible framework for practical, transparent and reproducible combination and comparison of ncRNA detection methods. We have proven the effectiveness of this approach in tests and by guiding experiments to find new ncRNAs. The software is freely available under the GNU General Public License (GPL), version 3 at webcite along with source code, screen shots, examples and tutorial material.