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knie

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Generate RNA logos with LogoGenerator
« on: September 22, 2016, 06:36:17 am »
Hi,

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

TIA.
Kate
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xiangjun

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Re: Generate RNA logos with LogoGenerator
« Reply #1 on: September 22, 2016, 10:29:37 am »
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.
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knie

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Re: Generate RNA logos with LogoGenerator
« Reply #2 on: September 22, 2016, 03:31:21 pm »
Hi Xiangjun,

Perfect! Many thanks for the prompt reply.

Best,
Kate
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knie

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Re: Generate RNA logos with LogoGenerator
« Reply #3 on: September 26, 2016, 06:03:44 pm »
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
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xiangjun

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Re: Generate RNA logos with LogoGenerator
« Reply #4 on: September 26, 2016, 11:18:16 pm »
Hi Kate,

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

Current (default settings):
Code: [Select]
/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

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
« Last Edit: September 27, 2016, 11:21:28 am by xiangjun »
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knie

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Re: Generate RNA logos with LogoGenerator
« Reply #5 on: September 27, 2016, 02:01:22 am »
Hi Xiang-Jun,

Got it! And thanks a lot for the information about logo colors :D

Best,
Kate
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