Workflow to identify rRF–target pairs in rRFtargetDB. Reference sequences obtained from NCBI and Ensembl (top right) are used to map chimeric reads and identify rRFs (top left) as described earlier (Guan and Grigoriev 2021). After mapping, targets are identified (center left), forward (rRF on the 5′ end and target on the 3′ end) and reverse (rRF on 3′ end and target on 5′ end) chimeric reads are used for grouping targets of each rRF. PAR-CLIP reads (center right) are used as evidence supporting the potential binding sites detected as common motifs in the targets of that rRF. Bottom dashed boxes illustrate the annotation of rRF–target pairs with MFE and motifs, clustering overlapping rRFs and linking the observed pairs to the rRNA genes and their secondary structure.
