Unipro UGENE User Manual
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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 each time.

This behavior may be corrected in future releases of UGENE.

DPI96

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.

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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 name 
  2. Molecule Topology (linear/circular). mfold gets sequence information from command line arguments. If the sequence is marked as circular Image Removed, then mfold will work with it as a circular one. Otherwise Image Removed, as with linear one.
    In the picture below, the sequence human_T1 is linear and therefore marked with the symbol Image Added, and CVU55762 with Image Added is circular.
    Image Added
    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
    Image Modified
  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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