Info
The tool was added in version 50.

The 'mfold' software is a tool for nucleic acid folding and hybridization prediction. It was developed by M. Zuker in the late 1980s for RNA folding and improved for DNA folding in 1996. mfold uses nearest neighbor energy rules.

UGENE itself must be installed to a path that does not contain non-printable characters or non-ASCII characters (Unicode characters). If installed incorrectly, a corresponding error while running the mfold task will be displayed.

Open the dialog

mfold only works with DNA or RNA sequences. You can trigger the dialog fromform
by selecting the appropriate Sequence View Global action
or through the Main Menu→Actions→Analyze
or through the Sequence Context Menu→Analyze

This is what the mfold dialog looks like
Image Removedlike on Windows OS

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	screenshot
	screenshot

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Input parameters

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This is the Settings section of the mfold settings tab.

Parameter	Unit	Default	Limits	Tool argument name	Description
Temperature	°C	37	[0,100]	T	The folding temperature. For RNA this is always the default value. For DNA it is taken from the dialog.
Ionic conditions	M	Na=1	[0,1.5]	NA_CONC	Ionic conditions are used to enter total monovalent (Na) and divalent (Mg) ions concentrations. For RNA this is always the default values. For DNA it is taken from the dialog.
Ionic conditions	M	Mg=0	[0,1.5]	MG_CONC
Percent suboptimality	%	5	[1,100]	P	The suboptimality percentage controls the free energy increment δδG for computing suboptimal foldings. Only foldings with a free energy ≤ΔG+δδG will be computed, where ΔG is the predicted minimum free energy. Normally, δδG=(P/100)\|ΔG\|, but it is rounded up to 1 kcal/mol or down to 12 kcal/mol if it is outside this range.
Max num of foldings		50	[1,100]	MAX	This is the maximum number of foldings that mfold will compute. It is better to limit the number of foldings by careful selection of the P and W parameters.
Window		0 (len≤29) 1 (30≤len≤49) 2 (50≤len≤119) 3 (120≤len≤199) 5 (200≤len≤299) 7 (300≤len≤399) 8 (400≤len≤499) 10 (500≤len≤599) 11 (600≤len≤699) 12 (700≤len≤799) 15 (800≤len≤1199) 20 (1200≤len≤1999) 25 (2000≤len)	[0,50]	W	The window parameter, W, controls the number of foldings that are computed. It may be thought of as a distance parameter. The distance between 2 base pairs, r_i r_j and r_i' r_j' may be defined as max{\|i-i′\|, \|j-j′\|}. If k-1 foldings have already been predicted by mfold, the kth folding must have at least W base pairs that are at least a distance W from any of the base pairs in the first k-1 foldings. A new folding is not added to the output list unless this criterion is fulfilled. As W increases, the number of predicted foldings decreases. A smaller value of this parameter will usually result in more computed foldings that may be quite similar to one another. A larger value will result in fewer foldings that are very different from one another. If the parameter is set to the default value, then in the calculations the real value of W will be set according to the described algorithm, based on the length of the selected region of the input sequence (see the Default column).
Max base pair distance		∞	[1,∞]	MAXBP	If the maximum distance between paired bases parameter, MAXBP, is specified, then any base pair, r_i r_j, in a folding must satisfy j-i≤MAXBP for a linear sequence or min{j-i, len+i-j}≤MAXBP, for a circular sequence (len is the length of the selected region of the input sequence). Thus small values of MAXBP ensure that only short range base pairs will be predicted. For example, in a sequence of 1000 nucleotides, setting MAXBP to 50 will force mfold to compute foldings involving only short range base pairs. The default is MAXBP=∞, which means no constraint.

Display settings

Corresponds to the Extended settings section on the main tab.

Parameter	Unit	Default	Limits	Tool argument name	Description
Base numbering frequency		10 (len≤50) 20 (51≤len≤300) 50 (301≤len)	[0,1000]	LAB_FR	Each image marks the number of the base (nucleotide) starting from the beginning 5'. The frequency with which this number will be displayed on an image depends on this parameter: if it is 0, then the number will not appear anywhere Image Modified if it is equal to 1, then each base will have its own number Image Modified if it is equal to 2, then each even base will have a number Image Modified and so on. Compare images above with the same algorithm settings to see the difference.

Rotation angle°0[-180,180]ROT_ANGSpecifying the orientation of the

If the parameter is set to the default value, then in the calculations the real value of LAB_FR will be set according to the described algorithm, based on the length of the selected region of the input sequence (see the Default column).
Rotation angle	°	0	[-180,180]	ROT_ANG	Specifying the orientation of the folded molecule by selecting the rotation angle. Positive values correspond to counter-clockwise.

Region settings

Specifies the part of the sequence that will be analyzed. The tool will only work with this piece of the sequence in isolation from the whole sequence.

...

If several regions have been selected in a sequence (using the GenBank format), then the dialog will only accept the first of them. The remaining selected regions are ignored. But there is an exception: if the sequence is marked circular and the region passing through the end/beginning is selected, then such a region is considered as a whole region and mfold will be launched on it as on an ordinary piece of the sequence (2 parts of the region – one that goes to end and another that starts from the beginning of the sequence – will be combined into one sequence and analyzed). This is the only case where the start of a region can be greater than the end:

Image RemovedImage Added Image RemovedImage Added

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	linear-circular
	linear-circular

A linear sequence is marked with the symbol

and for it the region 70..50 is invalid. A circular sequence is marked with the symbol

and for it the region 70..50 is valid.
The length of the region in this case 70..50 depends on the sequence length.

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Parameter

Default

Description

Save output to

/path/to/sequence/

The folder where the "mfold" subdirectory will be created with the output data in it. By default, this folder is the same as the folder where the input sequence is stored.

For example, let's say our OS is Windows and the analyzed sequence has the path "C:\path\to\sequence\my_sequence.fa". After running the task, the folder structure will look something like this

Code Block

C:.
└───path
    └───to
        └───sequence
            │   my_sequence.fa
            │
            └───mfold
                └───2024.03.19_16-31-34
                        inp.fa_1.pdf
                        inp.fa_1.png
                        inp.fa_2.pdf
                        inp.fa_2.png
                        inp.fa_3.pdf
                        inp.fa_3.png
                        out.html

The output folder must have write permissions.info

Settings are not saved between dialog calls. If you need to change the output folder to something other than the default, you will have to do this manually every time you call the dialog.

This behavior may be corrected in future releases of UGENE.

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	dpi
	dpi

DPI

96

Setting up the Ghostscript converter from PS files to PNG. Quality of saved images (PNG files). The higher this parameter, the higher the quality, size and resolution of the resulting images.

Info
This setting only affects images in the output folder. This setting does not affect images in the UGENE report. This setting does not affect PDF output files.

	Save states	Reset states
Algorithm settings	yes (it can be tedious to enter fields every time)	yes
Display settings	yes (it can be tedious to enter fields every time)	yes
Region	no (since the region is optionally selected manually by the user)	no (the same reason)
Output settings	yes	no (these unique settings are changed manually by the user when the user really needs it; a quick reset only makes sense for algorithmic settings)

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Old Version 16

New Version Current

Key

Open the dialog

Input parameters

Display settings

Region settings

Internal parameters

Saving/resetting dialog state

Output data

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Versions Compared

Old Version 16

New Version Current

Key

Open the dialog

Input parameters

Display settings

Region settings

Internal parameters

Saving/resetting dialog state

Output data