Unipro UGENE User Manual
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Table of Contents
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Prerequisites

For mfold to work correctly, the path to the temporary directory must not contain spaces, non-printable characters and non-ASCII characters (Unicode characters such as emoji, Cyrillic, Chinese family of scripts, etc.). In this case, you need to change the path to the temporary directory in the appropriate setting.

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 will be displayed.

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             

...

Corresponds to the Extended settings section on the main tab.

ParameterUnitDefaultLimitsTool argument nameDescription
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 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.

You can select the entire sequence, a custom region, or a selected region if there was one. The region must be less than 3000 bases. It is acceptable to select a small region (<10bp), but there will almost certainly be no folding there.

Rules for substituting the selected region:

  1. 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.
  2. The first rule has 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).

Output settings

UGENE&Ghostscript settings in the "Output" tab.

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 UGENE. This setting does not affect PDF.


Tool comparison

хранение результатов

подключение к интернету

какие настройки есть

исправлены баги

размер входных последовательностей


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