Bioinformatics of prokaryotic RNAs

Abstract

The genome of most prokaryotes gives rise to surprisingly complex transcriptomes, comprising not only protein-coding mRNAs, often organized as operons, but also harbors dozens or even hundreds of highly structured small regulatory RNAs and unexpectedly large levels of anti-sense transcripts. Comprehensive surveys of prokaryotic transcriptomes and the need to characterize also their non-coding components is heavily dependent on computational methods and workflows, many of which have been developed or at least adapted specifically for the use with bacterial and archaeal data. This review provides an overview on the state-of-the-art of RNA bioinformatics focusing on applications to prokaryotes.

Keywords: :

• RNA bioinformatics
• RNA–RNA interaction
• TSS annotation
• gene finding
• secondary structure prediction
• target prediction

10.4161/rna.28647

Disclosure of Potential Conflicts of Interest

No potential conflicts of interest were disclosed.

Acknowledgments

This work was supported by the DFG under the auspices of Priority Program SPP 1258: Sensory and regulatory RNAs in Prokaryotes, grant nos. BA 2168/2 and STA 850/7.