Bacterial genomes encode a plethora of small RNAs (sRNAs), which are heterogeneous in size, structure, and function. Most sRNAs bind to mRNA targets by means of specific
base-pairing interactions, and thereby act as post-transcriptional regulators, modifying translation or stability of the mRNA. The prediction of sRNA targets is therefore
a promising avenue to learn about the function of novel sRNAs.
Several approaches for the energy-based prediction of RNA-RNA interactions have been developed over the past years. Ideally, such methods should take into account the
competition of intra- and inter-molecular structure formation. Such accessibility based methods are, however, computationally more expensive. I will introduce our improved
RNAplex method, which uses an approximate energy model in order to achieve the same time complexity as simple sequence alignment, while still using accessibility.
In addition, we will present an RNAplex based web service for the bacterial sRNA target prediction in all currently available bacterial genomes. Finally, we will discuss
implications for the number of sRNA targets and the role of sRNA in regulatory networks.