Ebbie-MM 4.3
:: DESCRIPTION
Ebbie-MM (Ebbie-(mis)match) is a software that analyzes single mismatches of small RNAs to the genome of origin. Using Ebbie-MM, we analyzed a dataset of 7,790 non-redundant small RNAs cloned from Oryza sativa. In this limited dataset, we found 230 1-nt-mismatches of which only 19 % overlapped to themselves. Even with this very limited dataset of 43 overlapping 1-nt-mismatches, RNA base modifications were detectable in small RNAs. Thus, not all sequencing errors should be discarded as they could contain valuable information on RNA base modifications.
::DEVELOPER
H Alexander Ebhardt , Herbert H. Tsang and Denny C. Dai .
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Windows / MacOsX / Linux
- Java
- NCBI-Blast
:: DOWNLOAD
:: MORE INFORMATION
Citation
H. Alexander Ebhardt, Herbert H. Tsang, Denny C. Dai, Yifeng Liu, Babak Bosta3 and Richard P. Fahlman
Meta-analysis of small RNA-sequencing errors reveals ubiquitous post-transcriptional RNA modifications
Nucl. Acids Res. (2009) 37 (8): 2461-2470