# 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 — Character vector or string containing 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 `i`th residue in the RNA sequence `Seq` is paired with the `j`th 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

Example 81. 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);`
Example 82. 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 = ((((....))))``` 