miRAW: A deep learning-based approach to predict microRNA targets by analyzing whole microRNA transcripts
Fig 2
Examples of the types of miRNA binding sites considered by different candidate site selection methods (CSSMs).
(a) Potential canonical binding site accepted by the PITA, TargetScan (TS), and miRAW CSSMs. Here, the seed region contains a perfect 7mer. (b) Potential non-canonical compensatory binding site accepted by TS and miRAW CSSMs. The missing nucleotide pair in the seed region is compensated by the 9 consecutive pairs starting at position 10—centered pairing requires at least a 4mer at positions 10 to 14. (c) Potential non-canonical centered target site accepted by TS and miRAW CSSMs. The lack of perfect seed matching is compensated by additional consecutive pairs in nucleotides 9 to 12. (d) Potential non-canonical sites accepted only by the miRAW CSSMs. The extended seed region (10 nucleotides) and the inclusion of wobbles allows these scenarios to be considered as potential target sites.