RNAlib-2.4.3
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The Dot-Bracket notation as introduced already in the early times of the ViennaRNA Package denotes base pairs by matching pairs of parenthesis ()
and unpaired nucleotides by dots .
.
Example: A simple helix of size 4 enclosing a hairpin of size 4 is annotated as
((((....))))
A more generalized version of the original Dot-Bracket notation may use additional pairs of brackets, such as <>
, {}
, and []
, and matching pairs of uppercase/lowercase letters. This allows for anotating pseudo-knots, since different pairs of brackets are not required to be nested.
Example: The follwing annotations of a simple structure with two crossing helices of size 4 are equivalent:
<<<<[[[[....>>>>]]]] ((((AAAA....))))aaaa AAAA{{{{....aaaa}}}}
The WUSS notation, as frequently used for consensus secondary structures in Stockholm 1.0 format 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, ~
.
Pseudo-knots
The WUSS notation allows for annotation of pseudo-knots using pairs of upper-case/lower-case letters.
Example: <<<_AAA___>>>aaa