RNA-bioinformatics: tools, services and databases for the analysis of RNA-based regulation


  • R. Backofen
  • J. Engelhardt
  • A. Erxleben
  • J. Fallmann
  • B. Grüning
  • U. Ohler
  • N. Rajewsky
  • P.F. Stadler


  • Journal of Biotechnology


  • J Biotechnol 261: 76-84


  • The importance of RNA-based regulation is becoming more and more evident. Genome-wide sequencing efforts have shown that the majority of the DNA in eukaryotic genomes is transcribed. Advanced high-throughput techniques like CLIP for the genome-wide detection of RNA-protein interactions have shown that post-transcriptional regulation by RNA-binding proteins matches the complexity of transcriptional regulation. The need for a specialized and integrated analysis of RNA-based data has led to the foundation of the RNA Bioinformatics Center (RBC) within the German Network of Bioinformatics Infrastructure (de.NBI). This paper describes the tools, services and databases provided by the RBC, and shows example applications. Furthermore, we have setup an RNA workbench within the Galaxy framework. For an easy dissemination, we offer a virtualized version of Galaxy (via Galaxy Docker) enabling other groups to use our RNA workbench in a very simple way.