Parenthesis representation


Every base pair in the secondary structure is represented by an opening parenthesis ‘(‘and a closing parenthesis ‘)’. A single nucleotide which is not paired is marked by a dot ‘.’. The structure is then obtained by sliding through the entire sequence from 5’ to 3’ and placing ‘(‘ , ‘)’ or ‘.’  (figure 1). It is important to note that each RNA secondary structure has only one parenthesis representation and each parenthesis representation specifies only one RNA secondary structure.


Figure 1

 A tRNA secondary structure and its corresponding parenthesis representation