Unipro UGENE User Manual
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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.

Tool home page: mfold.org. Similar results to those produced by UGENE can be obtained using the mfold web server (DNA prediction, RNA prediction) or using the OligoAnalyzer tool. For complete documentation on the tool, see a) on the website, b) in the article, c) in the source code in the corresponding folder.

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Open the dialog

mfold only works with DNA or RNA sequences. You can trigger the dialog from
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

Input parameters

The tool is passed explicit and implicit parameters. Explicit parameters are set in the dialog, implicit parameters are taken from the sequence context.

Algorithm settings

For complete settings details, see the documentation on the mfold website or documentation in source.

This is the Settings section of the mfold settings tab.

ParameterUnitDefaultLimitsTool argument nameDescription
Temperature°C37[0,100]T

The folding temperature

is fixed at 37°C for RNA, but can take any integer value within acceptable limits for DNA

.

For RNA this is always the default value. For DNA it is taken from the dialog.

Ionic conditionsMNa=1[0,1.5]

NA_CONC

Ionic conditions are used to enter total monovalent (

for

Na) and divalent (Mg) ions concentrations.

Ionic conditions may be altered for DNA folding only.

For RNA

, the ionic conditions are fixed in

this is always the default values. For DNA it is taken from the dialog.

Mg=0MG_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.






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