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Tool home page: mfold.org.

UGENE uses Ghostscript to convert PS files to PNG and PDF.

ToC

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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

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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 
   Image Modified
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
   
3. 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.

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Example of a report on Windows (appearance may vary slightly between systems):

Image RemovedImage Added

1. Status, Time, … At the beginning there is information about the run: information about the task, settings for launch.
2. Output HTML report. Clickable link to the output HTML report. More about this report in the next section.
3. Found structures. List of found structures. The structure is characterized by free energy. When clicked, UGENE will scroll the window to the desired structure.
4. Structure table. The table contains
   1. Thermodynamic details: free energy, enthalpy, entropy and an estimated T_m.
   2. Loop Free-Energy Decomposition: the entire decomposition of the particular folding into loops and stacks, together with their free energies and closing base pairs. Consecutive runs of base pairs are summarized as helices.
   3. Image. Displays of nucleic acid secondary structure. At the bottom of the image there is information identifying it: free energy, name of the input sequence and region of analysis.
5. mfold log. Information about launching the external mfold tool: launch command and log.

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HTML report

A single HTML report and PNG+PDF for each structure found are saved in the output folder. The HTML report displays these images, PDFs and detailed information about the launch in an easy-to-view form.

Tool comparison

хранение результатов

подключение к интернету

какие настройки есть

исправлены баги

размер входных последовательностей

LinksImage AddedThis version of the report also contains:

1. Launch information.
2. List of found structures with links to them.
3. Information about each structure. The Loop Free-Energy Decomposition is located under the "Show structure detailed info" arrow.
   The quality of the images in the report depends on the DPI setting in the dialog. When you click on the picture, a PDF file with a structure image opens in a new tab, identical to the picture image, but allows you to zoom without losing quality.
4. mfold log.

This report is portable, i.e., if the directory is completely copied (HTML+all PNGs+all PDFs), the copied data can be re-opened in the browser without loss of functionality. Folders can be deleted/renamed; it will not affect the operation of UGENE.

Temporary output

mfold produces many files. Not all of them are displayed in the reports. However, while the current UGENE session is open, you can see what other files mfold produces.

In the Log corresponding to the [Algorithms][DETAILS] subcategories, you can see the mfold launch command. It depends on where the UGENE temporary directory is set. For example, it might look like this

"C:\Program Files\Unipro UGENE\tools\mfold\mfold.bat" SEQ=C:\tmp\ugene_tmp\p14120\mfold\d_0\inp.fa RUN_TYPE=html NA=DNA LC=circular T=37 P=5 NA_CONC=1 MG_CONC=0 MAX=100 ROT_ANG=0

In this case, all temporary output files will be located in C:\tmp\ugene_tmp\p14120\mfold\d_0. For information about the purpose and format of this data, please read the article.

Tool comparison

As mentioned earlier, the mfold tool can also be launched from the native site or from the IDT platform.

https://en.wikipedia.org/wiki/List_of_RNA_structure_prediction_software

References

1. Article https://www.ncbi.nlm.nih.gov/pmc/articles/PMC169194/
2. mfold home http://www.unafold.org/
3. mfold DNA http://www.unafold.org/mfold/applications/dna-folding-form.php
4. mfold RNA http://www.unafold.org/mfold/applications/rna-folding-form.php
5. mfold sources http://www.unafold.org/mfold/software/download-mfold.php
6. mfold settings documentation http://www.unafold.org/mfold/documentation/mfold-documentation.php
7. Viewing launch results http://www.unafold.org/cgi-bin/view-folds.cgi
8. Forum with mfold authors http://www.unafold.org/forum/
9. mfold references http://www.unafold.org/mfold/documentation/mfold-references.php
10. implementation of mfold by IDT company https://www.idtdna.com/calc/analyzer