Freiburg RNA tools: a central online resource for RNA-focused research and teaching

Martin Raden; Syed M Ali; Omer S Alkhnbashi; Anke Busch; Fabrizio Costa; Jason A Davis; Florian Eggenhofer; Rick Gelhausen; Jens Georg; Steffen Heyne; Michael Hiller; Kousik Kundu; Robert Kleinkauf; Steffen C Lott; Mostafa M Mohamed; Alexander Mattheis; Milad Miladi; Andreas S Richter; Sebastian Will; Joachim Wolff; Patrick R Wright; Rolf Backofen

doi:10.1093/nar/gky329

Freiburg RNA tools: a central online resource for RNA-focused research and teaching

Nucleic Acids Res. 2018 Jul 2;46(W1):W25-W29. doi: 10.1093/nar/gky329.

Authors

Martin Raden¹, Syed M Ali¹, Omer S Alkhnbashi¹, Anke Busch², Fabrizio Costa³, Jason A Davis⁴, Florian Eggenhofer¹, Rick Gelhausen¹, Jens Georg⁵, Steffen Heyne⁶, Michael Hiller^{7

8}, Kousik Kundu^{9

10}, Robert Kleinkauf¹, Steffen C Lott⁵, Mostafa M Mohamed¹, Alexander Mattheis¹, Milad Miladi¹, Andreas S Richter¹¹, Sebastian Will¹², Joachim Wolff¹, Patrick R Wright¹³, Rolf Backofen^{1

14}

Affiliations

¹ Bioinformatics, Computer Science, University of Freiburg, Georges-Koehler-Allee 106, 79110 Freiburg, Germany.
² Institute of Molecular Biology (IMB), Ackermannweg 4, 55128 Mainz, Germany.
³ Department of Computer Science, University of Exeter, Exeter EX4 4QF, UK.
⁴ Coreva Scientific, Kaiser-Joseph-Str 198-200, 79098 Freiburg, Germany.
⁵ Genetics and Experimental Bioinformatics, University of Freiburg, Schänzlestraße 1, 79104 Freiburg, Germany.
⁶ Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, 79108 Freiburg, Germany.
⁷ Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
⁸ Max Planck Institute for the Physics of Complex Systems, Dresden, Germany.
⁹ Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK.
¹⁰ Department of Human Genetics, The Wellcome Trust Sanger Institute, Hinxton Cambridge CB10 1HH, UK.
¹¹ Genedata AG, Margarethenstrasse 38, 4053 Basel, Switzerland.
¹² Theoretical Biochemistry Group, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria.
¹³ Department of Clinical Research, Clinical Trial Unit, University of Basel Hospital, Schanzenstrasse 55, 4031 Basel, Switzerland.
¹⁴ Centre for Biological Signalling Studies (BIOSS), University of Freiburg, Schaenzlestr. 18, 79104 Freiburg, Germany.

Abstract

The Freiburg RNA tools webserver is a well established online resource for RNA-focused research. It provides a unified user interface and comprehensive result visualization for efficient command line tools. The webserver includes RNA-RNA interaction prediction (IntaRNA, CopraRNA, metaMIR), sRNA homology search (GLASSgo), sequence-structure alignments (LocARNA, MARNA, CARNA, ExpaRNA), CRISPR repeat classification (CRISPRmap), sequence design (antaRNA, INFO-RNA, SECISDesign), structure aberration evaluation of point mutations (RaSE), and RNA/protein-family models visualization (CMV), and other methods. Open education resources offer interactive visualizations of RNA structure and RNA-RNA interaction prediction as well as basic and advanced sequence alignment algorithms. The services are freely available at http://rna.informatik.uni-freiburg.de.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Base Sequence / genetics*
Internet*
Nucleic Acid Conformation
RNA / chemistry
RNA / genetics*
Sequence Alignment / instrumentation
Sequence Analysis, RNA / instrumentation
Software*
Structure-Activity Relationship

Substances

RNA