AptBacterialDB

Understanding the Three Representations

Dot-Bracket Notation

A text-based representation of RNA/DNA secondary structure using ( ) for paired bases and . for unpaired bases.

Example: ((....)).. → stem → loop → stem

Strand Notation

A numeric representation where each position indicates the index of its paired base, or 0 if unpaired.

Example: 0 64 63 62

Element String

A label assigned to each nucleotide based on its structural role.

S = stem, H = hairpin, B = bulge, I = internal loop, M = multiloop, E = exterior

Example: ssmmmmss