Freiburg RNA Tools: a web server integrating INTARNA, EXPARNA and LOCARNA

Abstract

The Freiburg RNA tools web server integrates three tools for the advanced analysis of RNA in a common web-based user interface. The tools IntaRNA, ExpaRNA and LocARNA support the prediction of RNA-RNA interaction, exact RNA matching and alignment of RNA, respectively. The Freiburg RNA tools web server and the software packages of the stand-alone tools are freely accessible at http://rna.informatik.uni-freiburg.de.

Figure 1.

Screenshot of the IntaRNA result page for a set of example sequences. The table summarizes all predicted interactions including one suboptimal interaction for mRNA seq3. It can be sorted by clicking on the header of a column. The interaction shown below the table is highlighted in green. For this prediction, additional information such as interaction positions and different contributions of the interaction energy score are given.

Figure 2.

(a) Annotated structures from the ExpaRNA output. Regions of exact pattern matches (EPMs) have the same colour. Shown are two bacterial RNase P RNAs (left: A-type P RNA from Escherichia coli; right: B-type P RNA from Bacillus subtilis). Structures are taken from RNase P database (19). The numbers indicate four large EPMs. (b) Workflow for combining ExpaRNA with LocARNA. First ExpaRNA is called on the input RNAs to predict EPMs 1–4. This information is used as anchor constraints for a complete sequence–structure alignment by LocARNA. EPM numbers and colours are taken from (a).

Figure 3.

Figures from the LocARNA result page of an example aligning SECIS elements. (a) Alignment with colour annotation showing the conservation of base pairs and annotated column identity as generated by RNAalifold. (b) 2D plot of consensus secondary structure predicted from (a), using the same colour scheme.