# Documentation

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# rnaconvert

Convert secondary structure of RNA sequence between bracket and matrix notations

## Syntax

RNAStruct2 = rnaconvert(RNAStruct)

## Input Arguments

RNAStructSecondary 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 — Character vector 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 character vector 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 =

((((....))))