flattenDotBracket {ncRNAtools} | R Documentation |
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.
flattenDotBracket(extendedDotBracketString)
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. |
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 ("("-")").
https://www.tbi.univie.ac.at/RNA/ViennaRNA/doc/html/rna_structure_notations.html
# 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)