flattenDotBracket: Converts an extended Dot-Bracket secondary structure to basic...

In ncRNAtools: An R toolkit for non-coding RNA

Description

Generates a string with the secondary structure of an RNA sequence in the basic Dot-Bracket notation from a string in the extended Dot-Bracket notation.

Usage

flattenDotBracket(extendedDotBracketString)

Arguments

extendedDotBracketString

A string with a secondary structure representation of an RNA molecule in the extended Dot-Bracket notation. The extended Dot-Bracket notation uses dots (".") for unpaired bases, and multiple pairs of symbols ("("-")", "["-"]", ""-"", "<"-">", "A"-"a", "B"-"b", "C"-"c" and "D"-"d") to indicate paired bases. This allows the format to unambiguously represent highly nested structures, including pseudoknots.

Value

A string representing the secondary structure of the provided RNA in the basic Dot-Bracket format. In such format, dots (".") indicate unpaired bases, and paired bases are represented with pairs of round brackets ("("-")").

References

https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/rna_structure_notations.html

Examples

# A secondary structure string with characters other than dots and round 
# brackets, representing unambiguously pseudo-knots:

extendedDotBracketString <- "((((....((((.((((([[[[...)))))]]]]..)))).....))))."

# Convert it to the basic Dot-Bracket format:

basicDotBracketString <- flattenDotBracket(extendedDotBracketString)

ncRNAtools documentation built on Nov. 8, 2020, 8:14 p.m.