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Generate RNA logos with LogoGenerator

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knie:
Hi,

Is it possible to generate RNA logos with LogoGenerator? (i.e., display U instead of T)

TIA.
Kate

xiangjun:
Hi Kate,

Thanks for using the REDUCE Suite and for posting your question on the Forum.

Yes, LogoGenerator is applicable to RNA as well as DNA. You just need to specify an additional -rna option on the command-line, and everything else should work as expected. Please have a try and report back any issues you may have.

Best regards,

Xiang-Jun

PS. The REDUCE Suite has more features than those documented (with the command-line "-h" option). The default settings are designed to work for its advertised purpose only.

knie:
Hi Xiangjun,

Perfect! Many thanks for the prompt reply.

Best,
Kate

knie:
Hi Xiang-Jun,

As a followup question:
The default color of the nucleotide "U" from `LogoGenerator -rna` is light blue. Is it possible to change it to red (like the color of "T" in DNA logos)?

Best,
Kate

xiangjun:
Hi Kate,

Yes. You need to edit file $REDUCE_SUITE/html/LogoGenerator_PS.def slightly, as shown below.

Current (default settings):

--- Code: ---/colorDict <<
    (A) green       (a) m_green
    (C) blue        (c) m_blue
    (G) orange      (g) m_orange
    (T) red         (t) m_red
    (U) cyan        (u) m_cyan
    (X) white
>> def

--- End code ---

Change (U) cyan to (U) red will achieve what you asked. Of course, you can completely redefine the coloring scheme as you see fit in section "default color set".

A bit background info for the default colors: the A green, C blue, G orange, and T red coloring scheme follows WebLogo for DNA. On the other hand, the 3DNA software for 3D structures of DNA/RNA uses another convention: A red, C yellow, G green, T blue, and U cyan. See http://x3dna.org/articles/seeing-is-understanding-as-well-as-believing for some examples. So I ended up with cyan for U in RNA logo. Moreover, the REDUCE Suite Forum is based on the 3DNA Forum.

Best regards,

Xiang-Jun

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