Why is the y axis of the motif logo 2-bits?

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Hanwenheng Liu

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Jun 30, 2024, 12:56:31 AM (6 days ago) Jun 30

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Hi, sorry if this isn't exactly a MEME suite question. I'm wondering why does the y axis of the motif logo max out at 2, not 1? I found a blog on how the PWM is calculated, which seems to imply that log2 is used for convenience during the transformation from the frequency matrix. Is that why?

Thanks!

cegrant

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Jun 30, 2024, 1:06:00 AM (6 days ago) Jun 30

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We're happy to answer MEME Suite related questions, but this is really a general bioinformatics question. Take a look at the paper that introduced logos: Sequence logos: a new way to display consensus sequences.

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