Search rRFs and targets with flexible filters. (A) The search page with default filters indicated. (B) Output of the search results for rRFs from 28S rRNA that target mRNAs using binding motif (motif filter ON); only the first 20 lines are shown. Matching rRF sequences (Guide Seq) are shown, it is easy to see how they slightly overlap each other in this example. Each line corresponds to a UH (that refers to a pair of unique rRF sequences and unique target sequences) identified in a CLASH chimeric pair involving an rRF isoform and a target sequence. Result table is banded to highlight different pairs of rRFs and target genes. For example, 14 UHs (same rRF sequence, different target sequences) support the interaction between 28S-47-67 and target gene RPL41. Four UHs pass the filters (i.e., read count ≥ 5 and MFE ≤ −15) and shaded in the same color, to distinguish them from other pairs of rRFs and target genes. From-To indicate an rRF coordinate in the host rRNA and serves as a link to the rRF and target information (red box hyperlinks to Fig. 4). Target transcript, region of binding, name, and biotype are indicated, together with the counts of supporting UHs, read counts, and orientation (forward or reverse, see text).
