Freiburg RNA Tools: a web server for the computational analysis of non-coding RNAs

Many non-coding RNAs (ncRNAs) require a specific structure to perform their functions or interact via structural base pairing. Examples range from bacterial small RNAs, small nucleolar RNAs and spliceosomal RNAs to ribozymes and riboswitches. The analysis of these ncRNAs demands tools that take into account RNA structure.

We developed a series of tools for ncRNA analysis comprising prediction of RNA-RNA interaction (IntaRNA), exact RNA matching (ExpaRNA), and the multiple alignment of RNA (LocARNA). All tools are recently developed, continuously maintained and highly accurate, and, thus, have been used in recent studies. The Freiburg RNA tools web server (http://rna.informatik.uni-freiburg.de) gives access to these tools via an easy to use interface (1).
IntaRNA is a tool for the prediction of mRNA target sites for ncRNAs like eukaryotic microRNAs or bacterial small RNAs based on hybridization free energy and accessibility of the interaction sites (2). Recently, it was applied to identify two novel targets of the cyanobacterial RNA Yfr1 (3).
ExpaRNA is a tool for the fast comparison of two ncRNAs by identifying sequence-structure motifs common to both RNAs (4). Thus, it elucidates information about structural motifs that may remain hidden by sequence-structure alignment alone.
LocARNA is a tool for aligning multiple RNA sequences by simultaneous alignment and folding (5). It generates high quality alignments that take structural similarity into account.