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LogoGenerator background

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mparida:
Hi Xiang-Jun
The algorithm works great. I was able to generate ddG logos using this software. However, I was wondering if the LogoGenerator uses the deviation from the uniform background frequency (A,T,G,C), such as 0.25 to show over-represented and under-represented nucleotide frequency at each position. If so, is there an easy way to change it to the actual background frequency observed from our data instead. For example, instead of assuming the background frequency of A,T,G,C as 0.25 each can we change it to 0.20,0.20,0.30,0.30. Any help in this regard is appreciated.
 
Rocky

xiangjun:
Hi Rocky,

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

The LogoGenerator program simply uses the N-by-4 'PSAM' input data, with possible transformations (ddG, bits_info etc), to create a sequence logo. In essence, the program does not care about nucleotide frequency at each position, other than a log transformation for the ddG style.

To have full control of the logo-generation process, try the '-style=raw' option. You can then generate/edit the input data to LogoGenerator in whatever way that fits your purpose. Note also the Convert2PSAM utility program that may be helpful/convenient for the correct input format.

Hope this helps.

Xiang-Jun

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