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. 2015 Mar;21(3):333–346. doi: 10.1261/rna.044891.114

FIGURE 1.

FIGURE 1.

The RNAMotifScanX's algorithmic framework demonstrated by aligning two artificial motif instances. The output of the algorithm is the optimal alignment between the two input motifs in terms of a weighted combination of base-pairing, base-stacking, and primary sequence similarity.