rnaconvert - Convert secondary structure of RNA sequence between bracket and matrix notations

Syntax

RNAStruct2 = rnaconvert(RNAStruct)

Input Arguments

RNAStruct

Secondary structure of an RNA sequence represented by either: Bracket notation Connectivity matrix Tip   Use the rnafold function to create RNAStruct.

Output Arguments

RNAStruct2

Secondary structure of an RNA sequence represented by either: Bracket notation — String of dots and brackets, where each dot represents an unpaired base, while a pair of equally nested, opening and closing brackets represents a base pair. Connectivity matrix — Binary, upper-triangular matrix, where RNAmatrix(i, j) = 1 if and only if the ith residue in the RNA sequence Seq is paired with the jth residue of Seq.

Description

RNAStruct2 = rnaconvert(RNAStruct) returns RNAStruct2, the secondary structure of an RNA sequence, in matrix notation (if RNAStruct is in bracket notation), or in bracket notation (if RNAStruct is in matrix notation).

Examples

Converting from Bracket to Matrix Notation

1. Create a string representing a secondary structure of an RNA sequence in bracket notation.

   Bracket = '(((..((((.......)))).((.....)).))).';

2. Convert the secondary structure to a connectivity matrix representation.

   Matrix = rnaconvert(Bracket);

Converting from Matrix to Bracket Notation

1. Create a connectivity matrix representing a secondary structure of an RNA sequence.

       Matrix2 = zeros(12);
       Matrix2(1,12) = 1;
       Matrix2(2,11) = 1;
       Matrix2(3,10) = 1;
       Matrix2(4,9) = 1;

2. Convert the secondary structure to bracket notation.

   Bracket2 = rnaconvert(Matrix2)
   
   Bracket2 =
   
   ((((....))))

See Also

rnafold | rnaplot

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