CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains.

Patrick R Wright,Martin Mann,Rolf Backofen,Andreas S Richter,Steffen Lott,Dragos A Sorescu,Wolfgang R Hess,Jens Georg,Robert Kleinkauf

doi:10.1093/nar/gku359

Abstract

CopraRNA (Comparative prediction algorithm for small RNA targets) is the most recent asset to the Freiburg RNA Tools webserver. It incorporates and extends the functionality of the existing tool IntaRNA (Interacting RNAs) in order to predict targets, interaction domains and consequently the regulatory networks of bacterial small RNA molecules. The CopraRNA prediction results are accompanied by extensive postprocessing methods such as functional enrichment analysis and visualization of interacting regions. Here, we introduce the functionality of the CopraRNA and IntaRNA webservers and give detailed explanations on their postprocessing functionalities. Both tools are freely accessible at http://rna.informatik.uni-freiburg.de.

Highlights

In recent years, bacterial small RNAs have proven to be potent, versatile and important regulators of prokaryotic gene expression [1,2]
Bacterial small RNAs have proven to be potent, versatile and important regulators of prokaryotic gene expression [1,2]. They are extremely abundant in various prokaryotic genomes [3,4,5,6,7] and due to novel experimental [6,8,9] and computational [10,11,12] methods on the genomic scale, biologists are struggling with ever increasing magnitudes of sRNA data that can, in many cases, only be harnessed by bioinformatics analyses, preceding wetlab verifications
Several sRNA target prediction algorithms have been developed in the past [17], and many of them are available as webservers [14,18,19,20,21]

Summary

Introduction

Bacterial small RNAs (sRNAs) have proven to be potent, versatile and important regulators of prokaryotic gene expression [1,2]. Several sRNA target prediction algorithms have been developed in the past [17], and many of them are available as webservers [14,18,19,20,21]. We highlight that CopraRNA (Comparative prediction algorithm for small RNA targets) [22] and IntaRNA (Interacting RNAs) [23] produce more than sound results and supply postprocessing that greatly aids in the interpretation and evaluation of the results. While CopraRNA is a comparative method that constructs a combined sRNA target prediction for a set of given organisms, IntaRNA predicts interactions in single organisms.

Results

Conclusion