RNA-seq experiments are now routinely used for the large scale sequencing of transcripts. In bacteria or archaea, such deep sequencing experiments typically produce 10-50million fragments that cover most of the genome, including intergenic regions. In this context, the precise delineation of the non-coding elements is challenging. Non-coding elements include untranslated regions (UTRs) of mRNAs, independent small RNA genes (sRNAs) and transcripts produced from the antisense strand of genes (asRNA).
Now, researchers at Paris-Sud University have developed present a computational pipeline (DETR’PROK: detection of ncRNAs in prokaryotes) based on the Galaxy framework that takes as input a mapping of deep sequencing reads and performs successive steps of clustering, comparison with existing annotation and identification of transcribed non-coding fragments classified into putative 5′ UTRs, sRNAs and asRNAs. They provide a step-by-step description of the protocol using real-life example data sets from Vibrio splendidus and Escherichia coli.
Availability: The DETR’PROK pipeline is obtained from the Galaxy main tool shed (http://toolshed.g2.bx.psu.edu/)
- Toffano-Nioche C, Luo Y, Kuchly C, Wallon C, Steinbach D, Zytnicki M, Jacq A, Gautheret D. (2013) Detection of non-coding RNA in bacteria and archaea using the DETR’PROK Galaxy pipeline. Methods [Epub ahead of print]. [article]