The filling color problem of modified bases after DNA folding

[541]

When you fold the DNA, how do you change the color of each base? At present, only two colors can be modified. How to make different colors? I hope you can tell me the tutorial on how to modify the base color. I am looking forward to your reply. Thank you

[julie_huang]

Hi there, I have the similar question.
I hope different colors can be used when visualizing as jpg file.
I have found this option using command line:

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Usage: sir_graph [options] infile[.ct] | infile.ss
-col <color_file>	(User supplied color file.)
-col_ann <color_ann_file>	(As above for annotation colors)

However, I did not find an example color file or annotation file that goes with the input ".ct" file.

For example, if I have a ".ct" file as below:

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18      dG = 1.768       assay_fp
1       g       0       2       0       1       0       0
2       c       1       3       0       2       0       3
3       g       2       4       10      3       2       4
4       g       3       5       9       4       3       0
5       c       4       6       0       5       0       0
6       g       5       7       0       6       0       0
7       t       6       8       0       7       0       0
8       t       7       9       0       8       0       0
9       c       8       10      4       9       0       10
10      c       9       11      3       10      9       11
11      t       10      12      0       11      10      0
12      g       11      13      0       12      0       0
13      t       12      14      0       13      0       0
14      c       13      15      0       14      0       0
15      t       14      16      0       15      0       0
16      c       15      17      0       16      0       0
17      t       16      18      0       17      0       0
18      c       17      0       0       18      0       0

I plan to highlight the first 5 bases (gcggc) and last 5 bases (ctctc). How do I provide the "-col" color_file, or "-col_ann" file?

I noticed in the webpage version http://www.unafold.org/mfold/applicatio ... g-form.php
If I provide high-light as "1-5, 14-18", I can get the exact plot I want. I wonder how to do so using the "sir_graph" command line tool.

Thanks!