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General Discussion / LogoGenerator background
« on: May 15, 2019, 12:04:47 pm »
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
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