rnafold
Predict minimum freeenergy secondary structure of RNA sequence
Syntax
rnafold(
Seq
)
RNAbracket
= rnafold(Seq
)
[RNAbracket, Energy
] =
rnafold(Seq
)
[RNAbracket, Energy, RNAmatrix
]
= rnafold(Seq
)
...
= rnafold(Seq
,
...'MinLoopSize', MinLoopSizeValue
, ...)
...
= rnafold(Seq
,
...'NoGU', NoGUValue
, ...)
...
= rnafold(Seq
,
...'Progress', ProgressValue
, ...)
Input Arguments
Seq  Either of the following:

MinLoopSizeValue  Integer specifying the minimum size of the loops (in bases)
to be considered when computing the free energy. Default is 3 . 
NoGUValue  Controls whether GU or UG pairs are forbidden to form. Choices
are true or false (default). 
ProgressValue  Controls the display of a progress bar during the computation
of the minimum freeenergy secondary structure. Choices are true or false (default). 
Output Arguments
RNAbracket  Character vector of dots and brackets indicating the bracket notation for the minimumfree energy secondary structure of an RNA sequence. In the bracket notation, each dot represents an unpaired base, while a pair of equally nested, opening and closing brackets represents a base pair. 
Energy  Value specifying the energy (in kcal/mol) of the minimum freeenergy secondary structure of an RNA sequence. 
RNAmatrix  Connectivity matrix representing the minimum freeenergy secondary
structure of an RNA sequence. A binary, uppertriangular matrix where if and only if the i th
residue in the RNA sequence Seq is paired
with the j th residue of Seq . 
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 nearestneighbor approach.
Note
For long sequences, this prediction can be time consuming. For example, a 600nucleotide sequence can take several minutes, and sequences greater than 1000 nucleotides can take over 1 hour, depending on your system.
predicts
and returns the secondary structure associated with the minimum free
energy for the RNA sequence, RNAbracket
= rnafold(Seq
)Seq
, using
the thermodynamic nearestneighbor approach. The returned structure, RNAbracket
,
is in bracket notation, that is a 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.
[
also returns RNAbracket, Energy
] =
rnafold(Seq
)Energy
,
the energy value (in kcal/mol) of the minimum freeenergy secondary
structure of the RNA sequence.
[
also 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
if and only if the RNAmatrix
(i,
j) = 1i
th
residue in the RNA sequence Seq
is paired
with the j
th residue of Seq
.
... = rnafold(
calls Seq
, ...'PropertyName
', PropertyValue
,
...)rnafold
with optional properties
that use property name/property value pairs. You can specify one or
more properties in any order. Each PropertyName
must
be enclosed in single quotation marks and is case insensitive. These
property name/property value pairs are as follows:
specifies
the minimum size of the loops (in bases) to be considered when computing
the free energy. Default is ...
= rnafold(Seq
,
...'MinLoopSize', MinLoopSizeValue
, ...)3
.
controls
whether GU or UG pairs are forbidden to form. Choices are ...
= rnafold(Seq
,
...'NoGU', NoGUValue
, ...)true
or false
(default).
controls
the display of a progress bar during the computation of the minimum
freeenergy secondary structure. Choices are ...
= rnafold(Seq
,
...'Progress', ProgressValue
, ...)true
or false
(default).
Examples
Determine the minimum freeenergy secondary structure (in both bracket and matrix notation) and the energy value of the following RNA sequence:
seq = 'ACCCCCUCCUUCCUUGGAUCAAGGGGCUCAA';
[bracket, energy, matrix] = rnafold(seq);bracket
bracket =
..(((((...((....))...))))).....
References
[1] 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.
[2] 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