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

Background: 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. Results: 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 st...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Peter Raasch, Ulf Schmitz, Nadja Patenge, Julio Vera, Bernd Kreikemeyer, Olaf Wolkenhauer
• Keywords: BMCBI 2010, Detection, Streptococcus Pyogenes, Tools