Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline

Methods. 2013 Sep 1;63(1):60-5. doi: 10.1016/j.ymeth.2013.06.003. Epub 2013 Jun 25.


RNA-seq experiments are now routinely used for the large scale sequencing of transcripts. In bacteria or archaea, such deep sequencing experiments typically produce 10-50 million 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). Here we 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. We provide a step-by-step description of the protocol using real-life example data sets from Vibrio splendidus and Escherichia coli.

Keywords: Antisense RNA; Archaea; Bacteria; Non-coding RNA; Small RNA; Untranslated regions.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaea / genetics
  • Bacteria / genetics
  • Base Sequence
  • Computational Biology / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • RNA, Messenger / genetics
  • RNA, Messenger / isolation & purification*
  • RNA, Untranslated / genetics
  • RNA, Untranslated / isolation & purification*


  • RNA, Messenger
  • RNA, Untranslated