Unipro UGENE User Manual
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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.

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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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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:

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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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DPI
ParameterDefaultDescription
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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dpidpi96
Setting up the Ghostscript converter from PS files to PNG. Quality

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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.

For more information about output types, see the Output data section.

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  1. Molecule Type (DNA/RNA). mfold gets sequence information from command line arguments. Information about what type will be passed to the tool can be seen next to the sequence name
  2. Molecule Topology (linear/circular). mfold gets sequence information from command line arguments. If the sequence is marked as circular, then mfold will work with it as a circular one. Otherwise, as with linear one.
    Whether the sequence is linear/circular is described here.
    Part of a circular sequence will also be considered a circular sequence. If you want to change this behavior, uncheck "Mark sequence as circular" and then call the mfold dialog.
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    internal-dpi
    DPI of images in UGENE    . Ghostscript has a default DPI of 72. Therefore, this value is used for images for the internal UGENE report and this value cannot be changed.

Saving/resetting dialog state

Some dialog fields retain their state between dialog calls. For such fields, the ability to reset settings is also available (the "Reset settings" button at the bottom left in the screenshot of the dialog). Below is a table showing which states are saved between dialog calls and which of them can be reset to default values.


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

States are saved only for a specific sequence window. Thus, if you have two windows (or two views) for sequence-1 and one window for sequence-2, then each window will have its own state for the mfold dialog.

Output data

There are 3 types of output from the mfold task in UGENE:

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