Figure 1
From: A method for aligning RNA secondary structures and its application to RNA motif detection
RNA structure decomposition (A-B) and Partial structure determination (C-E). (A) A hypothetical RNA secondary structure is decomposed into a set of circles. (B) The circles are organized into a hierarchical tree. As shown, circle 8 contains only one pair of bases that are bonded with each other; therefore it corresponds to a loop. Circle 7 contains two pairs of bases that are bonded with each other respectively and also contains a single base (nucleotide C); therefore circle 7 corresponds to a bulge. Circle 6 corresponds to a stem of length two since it does not contain any single base. Circle 2 contains more than two pairs of bonded bases; therefore it corresponds to a junction. (C) A hypothetical RNA secondary structure is used to illustrate how partial structures are determined. (D) The partial structure for the single base G in boldface is shown. (E) The partial structure for the base pair C-G in boldface consists of two parts, a parent structure and a child structure. The base pair itself is included in the child structure.