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Entropy From Msa

Dear All

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

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updated by hadasa hadasa • written by User 0063 • User 0063

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written by Eric Normandeau Eric Normandeau

2 answers

I'm not sure that understand your question.

By definition:

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:

  1. gap is "nucleotide" then entropy = - sum(pa*loga+pc*logc+pg*logg+pt*logt+p_*log_)
  2. or skip gaps then entropy = - sum(pa*loga+pc(logc+pg*logg+pt*logt)

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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updated by Ram Ram • written by Alex Alex

look at this similar question Entropy From A Multiple Sequence Alignment With Gaps

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updated by Ram Ram • written by hadasa hadasa

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