Entropy From Msa
I'd like to write an algorithm to calculate Shannon Entropy in an MSA.
How can I consider gaps and colums fully conserved?
Thanks in advance
I'm not sure that understand your question.
Shannon_column_entropy = - sum(px*log(px)), where px - a frequency of each nucleotide.
MSA_entropy = sum(Shannon_column_entropies)
With gaps you have two alternatives:
- gap is "nucleotide" then entropy =
- or skip gaps then entropy =
If Shannon_column_entropy = 0 then a column is fully conserved.
And check this question Entropy From A Multiple Sequence Alignment With Gaps
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