Background letter frequencies
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3.8 years ago

I have a set of PWM matrix compressing of list of motifs from different sources. But confused with the Background letter frequencies. Because on some cases it is uniform for all the letter (i.e. 0.25 for each) and in some PWM these are of some other value.

Can anyone clarify how to calculate them and is it necessary for FIMO input?

Thanks in advance!

MEME FIMO Motif • 790 views
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