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Fig. 3 | BMC Bioinformatics

Fig. 3

From: Plant organelle RNA editing and its specificity factors: enhancements of analyses and new database features in PREPACT 3.0

Fig. 3

The new “pie-chart” mode for graphic display of RNA editing patterns allows to distinguish RNA editing events in first, second and third codon positions. Three sections (upper left, upper right and lower third) of a circle symbolize codon positions 1, 2 and 3, respectively. Forward and backward arrowheads indicate stop codons removed or introduced by RNA editing (see legend on top). In the query form (Additional file 1) users may adjust symbol sizes and different colours for C-to-U (here: blue) or U-to-C (here: red) RNA editing events and a threshold for highlighting edits shared between taxa by grey background shading (here: 2). Individual graphic displays are produced for each reference in the query, here exemplarily shown for the Marchantia polymorpha reference in the mitochondrial atp9 example (Additional file 1). Editing site labels are indicated upon mouse-over at the editing symbols. Boxes and three-letter-acronyms are here added to designate the seven major plant clades: angiosperms (ANG), gymnosperms (GYM), ferns (FER), lycophytes (LYC), hornworts (HOR), mosses (MOS) and liverworts (LIV). The purple arrow at the bottom points to editing event atp9eU92SL conserved among many taxa and for which PpPPR_98 has been characterized as an editing factor in Physcomitrella (see Fig. 5a)

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