How to calculate the entropy of a DNA sequence - and/or it's complexity
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2.4 years ago


I am trying to propose a way to show that a given sequence, given to another one is less/more complex. I would like to explain by this that some mapping issues can come from there. I'd like to show it with a 4 letters genome, and a 3 letters genome (bisulfite converted).

I heard that shannon's entropy can help me in that, but I am actually not very sure. 1) it seems it works fine to find motifs, to find what's possibly common when comparing sequences ( and I think I quite understand how it is calculated.

2) I have found some formulas and calculator to calculate a general entropy ( ) that is interesting and it may help me.

3) I was, however, thinking that maybe I could calculate an entropy factor for a given sequence regarding repeated motifs it may have ( like in this paper )

4) finally, but I think I can't find it back, I would have been in search for a 'by position' entropy, that would show a decrease of complexity in some parts of my sequences. It seems the package HDMD can help me, but again, I need to "compare" different sequences to have en entropy score.

Alternatively, if it's a bad way to assess complexity of sequencing (related to mapping), would you recommend something else?


WGBS DNA R genome • 2.5k views
Entering edit mode
2.4 years ago
onestop_data ▴ 300

Great question. Shannon Entropy should do the job to compute complexity for a DNA string. Here I share a script to do it.. I hope it helps.


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