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Figure 4 | BMC Bioinformatics

Figure 4

From: A method for aligning RNA secondary structures and its application to RNA motif detection

Figure 4

The two pattern-based RNA structures used in this study. (A) Histone 3'-UTR (HSL3) motif. (B) Iron Response Element (IRE) motif. A wildcard, represented by a lowercase letter n, is allowed to appear in a motif. When matching the motif with an RNA secondary structure, the wildcard in the motif can be instantiated into zero or one nucleotide in the secondary structure at no cost. Wildcards are used in places where the length of a region, either single-stranded or double-stranded, is variable. For example, the 5' flanking tail of HSL3 can be 4 or 5 nt long, and the lower part of the stem region of IRE can be 2 to 8 nt long.

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