Computational Tools for Predicting sRNA Targets

Abstract

Bacterial sRNAs are an emerging class of small regulatory RNAs of 40 to 500 nucleotides in length. They play a wide variety of important roles in many biological processes through binding to their mRNA or protein targets, such as expression regulation of outer membrane proteins, iron homeostasis, quorum sensing and bacterial virulence. Therefore, predicting sRNA targets plays a key role in elucidating sRNA functions. Here we intend to introduce some computational tools for predicting mRNA targets of sRNAs. Firstly, we will give an outline of some key concepts and programs associated with the prediction models developed by our center. Secondly, we will present detailed instructions on how to use the sRNATarget web server and the Perl program for both windows and the Linux system. Thirdly, we will briefly introduce the main ideas behind other tools, including IntaRNA and TargetRNA. Finally, we will present an outlook on future developments in the prediction of sRNA targets.