quick question about a degenerated position in motifs
Hi there
Supose You have a list of motifs and You want to get a consensus sequence and my question is:
in positions where there are degeneration can You choose any base right? But it is better to choose based on a nucleotide probability distribution, like, you get this probs from all the nucs in the motifs list. And then using something like this:
random.choices('ACGT', probs) ?
Or You simple uses random.choice('ACGT')?
Thanks
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Depends what the intended use is. You could pick the residue based on the most common, or you can use degeneracy characters if it's always a residue with a specific property etc.