RNA Secondary Structures#

Functions to create, parse, convert, manipulate, and compare secondary structure representations.

Dot-Bracket Notation#

WUSS Notation#

Washington University Secondary Structure (WUSS) notation related functions

Pair Tables#

Pair Table Representation of Secondary Structures

>>> import RNA
... # create a pair table from dot-bracket structure
... pt = RNA.ptable("(((.(((...))))))")
... # print each base pair
... for i, v in enumerate(pt[1:], start = 1):
...     if pt[i] > i:
...         print(f"base pair ({i},{pt[i]})")
...
base pair (1,16)
base pair (2,15)
base pair (3,14)
base pair (5,13)
base pair (6,12)
base pair (7,11)

Pair Lists#

Pair List Representation of Secondary Structures

Abstract Shapes#

Abstract Shapes Representation of Secondary Structures

Helix Lists#

Helix List Representation of Secondary Structures

Tree Representation#

Tree Representation of Secondary Structures

Distance measures#

Distance measures between Secondary Structures

Benchmarking#

Benchmarking Secondary Structure Predictions