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Nucleic Acids Res. 2014 Jul;42(Web Server issue):W119-23. doi: 10.1093/nar/gku359. Epub 2014 May 16.

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

Author information

1
Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany Genetics and Experimental Bioinformatics, Faculty of Biology, Schänzlestr. 1, D-79104 Freiburg, Germany.
2
Genetics and Experimental Bioinformatics, Faculty of Biology, Schänzlestr. 1, D-79104 Freiburg, Germany.
3
Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany.
4
Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51, D-79108 Freiburg, Germany.
5
Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany BIOSS Centre for Biological Signalling Studies, Cluster of Excellence, Albert-Ludwigs-University Freiburg, Germany Center for non-coding RNA in Technology and Health, University of Copenhagen, Gronnegardsvej 3, DK-1870 Frederiksberg C, Denmark ZBSA Centre for Biological Systems Analysis, Albert-Ludwigs-University Freiburg, Habsburgerstr. 49, D-79104 Freiburg, Germany backofen@informatik.uni-freiburg.de.

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.

PMID:
24838564
PMCID:
PMC4086077
DOI:
10.1093/nar/gku359
[Indexed for MEDLINE]
Free PMC Article

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