Washington University Secondary Structure (WUSS) notation

The WUSS notation, as frequently used for consensus secondary structures in Stockholm 1.0 format. More...

Detailed Description

The WUSS notation, as frequently used for consensus secondary structures in Stockholm 1.0 format.

This notation allows for a fine-grained annotation of base pairs and unpaired nucleotides, including pseudo-knots. Below, you'll find a list of secondary structure elements and their corresponding WUSS annotation (See also the infernal user guide at http://eddylab.org/infernal/Userguide.pdf)

• Base pairs
  Nested base pairs are annotated by matching pairs of the symbols <>, (), {}, and []. Each of the matching pairs of parenthesis have their special meaning, however, when used as input in our programs, e.g. structure constraint, these details are usually ignored. Furthermore, base pairs that constitute as pseudo-knot are denoted by letters from the latin alphabet and are, if not denoted otherwise, ignored entirely in our programs.

• Hairpin loops
  Unpaired nucleotides that constitute the hairpin loop are indicated by underscores, _.

  Example: <<<<<_____>>>>>

• Bulges and interior loops
  Residues that constitute a bulge or interior loop are denoted by dashes, -.

  Example: (((--<<_____>>-)))

• Multibranch loops
  Unpaired nucleotides in multibranch loops are indicated by commas ,.

  Example: (((,,<<_____>>,<<____>>)))

• External residues
  Single stranded nucleotides in the exterior loop, i.e. not enclosed by any other pair are denoted by colons, :.

  Example: <<<____>>>:::

• Insertions
  In cases where an alignment represents the consensus with a known structure, insertions relative to the known structure are denoted by periods, .. Regions where local structural alignment was invoked, leaving regions of both target and query sequence unaligned, are indicated by tildes, ~.

  Note

  These symbols only appear in alignments of a known (query) structure annotation to a target sequence of unknown structure.

• Pseudo-knots
  The WUSS notation allows for annotation of pseudo-knots using pairs of upper-case/lower-case letters.

  Note

  Our programs and library functions usually ignore pseudo-knots entirely treating them as unpaired nucleotides, if not stated otherwise.

  Example: <<<_AAA___>>>aaa

Collaboration diagram for Washington University Secondary Structure (WUSS) notation:

Functions
char *	vrna_db_from_WUSS (const char *wuss)
	Convert a WUSS annotation string to dot-bracket format. More...

Function Documentation

vrna_db_from_WUSS()

char * vrna_db_from_WUSS

(

const char *

wuss

)

#include <ViennaRNA/utils/structures.h>

Convert a WUSS annotation string to dot-bracket format.

Note

This function flattens all brackets, and treats pseudo-knots annotated by matching pairs of upper/lowercase letters as unpaired nucleotides

Parameters

wuss	The input string in WUSS notation

Returns

A dot-bracket notation of the input secondary structure