CopraRNA and IntaRNA: predicting small RNA targets, networks and interaction domains.
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.
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.
Patrick R
PR
Wright
Genetics and Experimental Bioinformatics, Faculty of Biology, Schänzlestr. 1, D-79104 Freiburg, Germany.
Jens
J
Georg
Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany.
Martin
M
Mann
Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany.
Dragos A
DA
Sorescu
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.
Andreas S
AS
Richter
Genetics and Experimental Bioinformatics, Faculty of Biology, Schänzlestr. 1, D-79104 Freiburg, Germany.
Steffen
S
Lott
Bioinformatics Group, Department of Computer Science, Albert-Ludwigs-University Freiburg, Georges-Köhler-Allee 106, D-79110 Freiburg, Germany.
Robert
R
Kleinkauf
Genetics and Experimental Bioinformatics, Faculty of Biology, Schänzlestr. 1, D-79104 Freiburg, Germany.
Wolfgang R
WR
Hess
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.
Rolf
R
Backofen
D000465:Algorithms; D053263:Gene Regulatory Networks; D020407:Internet; D012329:RNA, Bacterial / Q000737:chemistry* / Q000378:metabolism*; D058727:RNA, Small Untranslated / Q000737:chemistry* / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D012984:Software
D012329:RNA, Bacterial; D058727:RNA, Small Untranslated