Structure and interaction prediction in prokaryotic RNA Biology

Microbiol Spectr.           online article

Many years of research in RNA biology have soundly established the importance of RNA-based regulation far beyond most early traditional presumptions. Importantly, the advances in “ wet ” laboratory techniques have produced unprecedented amounts of data that require e ffi cient and precise computational analysis schemes and algorithms. Hence, many in silico methods that attempt topological and functional classi fi cation of novel putative RNA-based regulators are available. In this review, we technically outline thermodynamics-based standard RNA secondary structure and RNA-RNA interaction prediction approaches that have proven valuable to the RNA research community in the past and present. For these, we highlight their usability with a special focus on prokaryotic organisms and also brie fl y mention recent advances in whole-genome interactomics and how this may in fl uence the fi eld of predictive RNA research.