Bioinformatics Toolbox™

rnaconvert

Convert secondary structure of RNA sequence between bracket and matrix notations

Syntax

RNAStruct2 = rnaconvert(RNAStruct)

Arguments

RNAStruct

Secondary structure of an RNA sequence represented by either:

Bracket notation
Connectivity matrix

Tip Use the rnafold function to create RNAStruct.

Return Values

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

Create a string representing a secondary structure of an RNA sequence in bracket notation.
```
Bracket = '(((..((((.......)))).((.....)).))).';
```
Convert the secondary structure to a connectivity matrix representation.
```
Matrix = rnaconvert(Bracket);
```

Converting from Matrix to Bracket Notation

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;

Convert the secondary structure to bracket notation.