moses is a Java framework that allows the combination of ncRNA detections methods to scan genomes for novel ncRNA genes.

Contact
ulf.schmitz(at)uni-rostock.de

Systems Biology & Bioinformatics Group
University of Rostock


Results & Data

Publication

This section contains the additional files and data accompanying the submitted paper Raasch et al. "non-coding RNA detection methods combined to improve usability, reproducibility and precision."

Detection workflows for the case studies
- The complete workflow with parameters and all data calculated for the three genomes is available on the moses website...
Workflow
Escherichia Coli Results
Listeria monocytogenes Results
Streptococcus pyogenes Results

Test for influence of window size on individual methods
- We chose 75bp because it seems to produce almost as good results as 101bp but at lower computational costs. Data for these tests is also given on the moses website.
Test for influence of window size on individual methods

Test for influence of window size on combined method
- The resulting sequence of integer values from 0–4 were then scanned using another sliding window. We tried different window sizes and 75bp gave the best results (data given on the moses website).
Test data for influence of window size on combined method

Data for prediction of new ncRNA in Streptococcus Pyogenes
- To arrive at a candidate list that had the most potential to be true ncRNA genes—in order to minimize unsuccessful experiments—we used manual inspection of multiple data sources instead. All data calculated and the used parameters are available on the moses website.
- Data used for the visual inspection is available on the moses website.
- Corresponding screenshots of all four candidate regions and data used for primer design with genomic coordinates are given on the moses website.
- The combination of multiple methods, possible in moses, has yielded highly probable candidates. RNAz or BLAST alone, for instance, would have given us hundreds of candidate loci to examine (data on the moses website).
- (Figure 4) Screenshots for all four candidates are given on the moses website.
Data for prediction of new ncRNA in Streptococcus pyogenes

Procedure and data for experimental verification of candidates in Streptococcus pyogenes
- Details of the experimental procedure, including the used primers, are given on the moses website.
- (Figure 5) Analysis of RT-PCR products by agarose gel electrophoresis. Details of the experimental procedure are given on the moses website
Procedure and data for experimental verification of candidates in Streptococcus pyogenes