quick question about a degenerated position in motifs

Question

[psschlogl]

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

[Joe]

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.