BEAR (Brand nEw Alphabet for RNAs) is a new encoding allowing to store secondary structure information within a single string of characters. BEAR unambiguously associates information about secondary structure to each nucleotide in a RNA sequence. In the BEAR encoding, every letter carries the information about the length and type of structure it belongs to (e.g. 'a' identify a stem of length one). Differently from the dot-bracket notation, the assignment of each nucleotide to the secondary structure element it belongs to allows one to discriminate nucleotides described with the same symbol (a dot or a bracket) but belonging to a different secondary structure element. A BEAR representation of RNA secondary structure is a string, having the same length of the associated RNA sequence but, at the same time, encodes for more structural information than the standard dot-bracket notation. For instance, the BEAR encoding discerns unpaired nucleotides belonging to a loop and to a bulge.

For more information please check the documentation page.
To download the BEAR encoder please go to download page.