# rnafold

Predict minimum free-energy secondary structure of RNA sequence

## Syntax

## Description

`rnafold(`

predicts and displays the
secondary structure (in bracket notation) associated with the minimum free energy for the
RNA sequence, `Seq`

)`Seq`

, using the thermodynamic nearest-neighbor approach.

**Note**

For long sequences, this prediction can be time consuming. For example, a 600-nucleotide sequence can take several minutes, and sequences greater than 1000 nucleotides can take over 1 hour, depending on your system.

returns the secondary structure associated with the minimum free energy for the RNA
sequence, `RNAbracket`

= rnafold(`Seq`

)`Seq`

, using the thermodynamic nearest-neighbor approach. The
returned structure, `RNAbracket`

, is in bracket notation, that is a
vector of dots and brackets. Each dot represents an unpaired base, while a pair of equally
nested, opening and closing brackets represents a base pair.

`[`

returns `RNAbracket`

,`Energy`

] = rnafold(`Seq`

)`Energy`

, the energy value (in kcal/mol) of the minimum
free-energy secondary structure of the RNA sequence.

`[`

returns `RNAbracket`

,`Energy`

,`RNAmatrix`

] = rnafold(`Seq`

)`RNAmatrix`

, a connectivity matrix representing the secondary
structure associated with the minimum free energy. `RNAmatrix`

is an
upper triangular matrix where

only if the `RNAmatrix`

(i, j) = 1`i`

th residue in the RNA sequence `Seq`

is
paired with the `j`

th residue of `Seq`

.

`___ = rnafold(`

specifies options using one or more name-value arguments in addition to the input arguments
in previous syntaxes. Each name-value argument is case insensitive.`Seq`

,`Name=Value`

)

## Examples

## Input Arguments

## Output Arguments

## References

[1]

[2] Wuchty, S., Fontana, W., Hofacker, I., and Schuster, P. (1999).
Complete suboptimal folding of RNA and the stability of secondary structures. Biopolymers
*49*, 145–165.

[3] Matthews, D., Sabina, J., Zuker, M., and Turner, D. (1999).
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary
structure. J. Mol. Biol. *288*, 911–940.

## Version History

**Introduced in R2007b**