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. 2014 Apr 21;42(10):6146–6157. doi: 10.1093/nar/gku283

Figure 1.

Figure 1.

The BEAR encoding. (A) The BEAR structural alphabet. Different sets of characters are associated with the different RNA basic structures (loop, internal loop, stem and bulge on the right side of a stem, and bulge on the left side, denoted here as L, I, S,BL and BR, respectively), with different characters used for basic structures of different length. (B) RNA hairpin with the constituent substructures (loop, stem, bulges and internal loop) highlighted in different colors. On the top right, the BEAR characters corresponding to each substructure, shown with the same colors. On the bottom right, the hairpin RNA sequence is shown associated with its dot-bracket and its BEAR secondary structure descriptions. (C) Conversion into BEAR of an RNA secondary structure. An RNA secondary structure, extracted from Rfam, is shown, containing four non-branching structures depicted in boxes. The resulting BEAR conversion of the non-branching and branching structures is shown in blue below the secondary structure. A ‘:’ character is assigned to the remaining nucleotides that do not belong to non-branching or branching structures (reported in black).