Question: Entropy From Msa
0
gravatar for User 0063
8.3 years ago by
User 0063210
User 0063210 wrote:

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

multiple • 2.9k views
ADD COMMENTlink written 8.3 years ago by User 0063210

Hi! In order for the members of the forum to help you, you should define your problem better. Here are a few tips for writing better questions. 1) Describe what you are doing. For people to help you, they must have a good understanding of what you are trying to accomplish. 2) Describe what you have tried so far, so that you don't get answers that tell you to do stuff you have already done. 3) Ask a specific question, avoid asking everything at the same time. 4) In order to get informative answers, you must write informative and well formated questions. Cheers!

ADD REPLYlink written 8.3 years ago by Eric Normandeau10k
2
gravatar for Alex
8.3 years ago by
Alex1.4k
Theodosius Dobzhansky Center for Genome Bioinformatics
Alex1.4k wrote:

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(paloga+pclogc+pglogg+ptlogt+p_*log_)
  2. or skip gaps then entropy = - sum(paloga+pclogc+pglogg+ptlogt)

If Shannon_column_entropy = 0 then a column is fully conserved.

And check this question http://biostar.stackexchange.com/questions/3864/entropy-from-a-multiple-sequence-alignment-with-gaps

ADD COMMENTlink written 8.3 years ago by Alex1.4k
1
gravatar for hadasa
8.3 years ago by
hadasa1.0k
hadasa1.0k wrote:

look at this similar question http://biostar.stackexchange.com/questions/3864/entropy-from-a-multiple-sequence-alignment-with-gaps

ADD COMMENTlink written 8.3 years ago by hadasa1.0k
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