Fig. 5

a The example of PPR_98 targeting the atp9eU92SL editing site in Physcomitrella patens. PPR_98 is a typical DYW-type PPR protein with 21 canonical PLS repeats. Nine of its P- and S-type PPRs (bold) perfectly follow the core RNA recognition rules (green shading) with amino acids T or N in position 5 to select for purines vs. pyrimidines, respectively, and amino acids D or N in position L (“Last”) to select for keto vs. amino bases in the target RNA. Binding properties of L-type PPRs and the divergent terminal “S2-type” PPR linking to the E1 domain are not understood. We here suggest an annotation with reverse numbering of PPRs starting with the last repeat and indicating the amino acids in positions 5 and L as shown in the PPR labels under B. In three cases, nucleotides other than expected are juxtaposed with the target: A instead of the expected U in S-19 (transversion, red shading), G instead of A in S-10 (purine transition, yellow shading) and U instead of C in P-9 (pyrimidine transition, blue shading). b The TargetScan interface allows to set a length for a weighted nucleotide query (top left) which then becomes available for definition and adjustment in all positions (middle). An additional overall weighting can be given below for each position. The example shown reflects the deduced atpeU92SL target shown in A. Upon assigning a value (0–100%) for a given nucleotide identity it can be temporarily “locked” by a click (switching green to red), allowing for further adjustments of the remaining identities, which automatically add up to 100% for a given position. This is exemplarily shown for position − 1 where the empirically observed pyrimidine bias is here reflected by arbitrary weights fixed for A (15%), C (35%) and G (5%) to automatically set 45% for T. The example shows arbitrary adjustments for P- and S-type PPRs assuming a 90 vs. 10% selectivity between purines (T/S + N for A vs. T/S + D for G) and a 70 vs. 30% selectivity for pyrimidines (N + N/S for C vs. N + D for U). Positions identifying purines receive a double weight (200%), pyrimidines and position − 1 receive 100% weight. Selecting “Around editing sites” (top) allows to fix any site to be a documented edit within the PREPACT references (‘EdS’) by selecting a radio button. The Physcomitrella patens mitochondrial and chloroplast editome references are selected for querying. Mouse-over gives information on the respective reference, here shown for the Physcomitrella mtDNA. As an alternative to PREPACT’s editome references, users may upload alternative sequences for querying