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

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- A nd 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.