labelled DNA structure with different color

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zhaoyang
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Joined: 01/24/2011

Who can tell me how to labelled the DNA strcuture with different color as the structure shown in the page "Mfold web server"?
I only know use one color highlight the structure.

zukerm
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Joined: 11/12/2010
Color annotation of structures

The mfold web server allows users to highlight specified regions of an RNA or DNA sequence. In the structure plot, the specified regions are drawn in color. The other regions are drawn in black. This particular feature is not offered in the mfold or UNAFold packages that users can download.

The mfold and UNAFold software annotates secondary structures in color using either "P-num" information or probability information. A reference for this type of annotation is the article by Zuker & Jacobson listed on the mfold server reference page. A preprint of this article is located on this web site

By downloading the mfold_util package, you can generate any color annotation you wish using the sir_graph program together with an annotation file (.ann) that you create yourself. Unless you are able to do all of this for yourself, you not be able to generate annotation in different colors for arbitrary regions of a sequence. By the way, the Structure Display and Free Energy Determination allows you to enter a secondary structure as a ct file or as a .b (Vienna dot/bracket format) file. If the sequence length is no greater than 1500, color annotation by probabilities is given automatically. The structure on the home page of the mfold web server is colored by probabilities.