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R-chie: a web server and R package for visualizing cis and trans RNA-RNA, RNA-DNA and DNA-DNA interactions

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Item Type:Article
Title:R-chie: a web server and R package for visualizing cis and trans RNA-RNA, RNA-DNA and DNA-DNA interactions
Creators Name:Tsybulskyi, V. and Mounir, M. and Meyer, I.M.
Abstract:Interactions between biological entities are key to understanding their potential functional roles. Three fields of research have recently made particular progress: the investigation of transRNA-RNA and RNA-DNA transcriptome interactions and of trans DNA-DNA genome interactions. We now have both experimental and computational methods for examining these interactions in vivo and on a transcriptome- and genome-wide scale, respectively. Often, key insights can be gained by visually inspecting figures that manage to combine different sources of evidence and quantitative information. We here present R-chie, a web server and R package for visualizing cis and transRNA-RNA, RNA-DNA and DNA-DNA interactions. For this, we have completely revised and significantly extended an earlier version of R-chie (1) which was initially introduced for visualizing RNA secondary structure features. The new R-chie offers a range of unique features for visualizing cis and transRNA-RNA, RNA-DNA and DNA-DNA interactions. Particularly note-worthy features include the ability to incorporate evolutionary information, e.g. multiple-sequence alignments, to compare two alternative sets of information and to incorporate detailed, quantitative information. R-chie is readily available via a web server as well as a corresponding R package called R4RNA which can be used to run the software locally.
Source:Nucleic Acids Research
ISSN:0305-1048
Publisher:Oxford University Press
Volume:48
Number:18
Page Range:e105
Date:9 October 2020
Official Publication:https://doi.org/10.1093/nar/gkaa708
PubMed:View item in PubMed

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