rnaconvert

Convert secondary structure of RNA sequence between bracket and matrix notations

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    Syntax

    RNAStruct2 = rnaconvert(RNAStruct)

    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).

    example

    Examples

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    Open Live Script

    Create a character vector representing a secondary structure of an RNA sequence in bracket notation.

    Bracket = "(((..((((.......)))).((.....)).))).";

    Convert the secondary structure to a connectivity matrix representation.

    Matrix = rnaconvert(Bracket);
    Open Live Script

    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.

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

    Input Arguments

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    Input secondary structure of an RNA sequence, specified as a character vector or string (bracket notation) or a binary, upper-triangular matrix (matrix notation).

    • Bracket notation is a bracket of dots and brackets indicating the bracket notation. In the bracket notation, each dot represents an unpaired base, while a pair of equally nested, opening and closing brackets represents a base pair.

    • Connectivity matrix is a binary, upper-triangular matrix, where RNAStruct(i,j) = 1 if and only if the ith residue in the RNA sequence is paired with the jth residue of the sequence.

    Use the rnafold function to create RNAStruct.

    Data Types: double | char | string

    Output Arguments

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    Output secondary structure of an RNA sequence, returned as a character vector (bracket notation) or a binary, upper-triangular matrix (matrix notation).

    Version History

    Introduced in R2007b

    See Also

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