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Shannon Entropy for DNA

I have genome and patterns with 2, 4, 8, 16 lengths. I want to calculate entropy of each pattern in genome? How to calculate this? If you have some advice pls put it here and is it right way to calculate entropy for each pattern?

dna entropy
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written by markic • markic

Hi,

My patterns are for example: AC, GGCC, GAAAGGCG, GGACTAAATCCAGTTT or some random ... I have 10 patterns by each length.

I have ecoli genome in siple text format (not fasta): AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATATCA ....

Now i want to find entropy for each pattern in this genome.

Second question is hot to interpret that values?

• 1 views • link
written by markic • markic

Hi,

My patterns are for example: AC, GGCC, GAAAGGCG, GGACTAAATCCAGTTT or some random ... I have 10 patterns by each length.

I have ecoli genome in siple text format (not fasta): AGCTTTTCATTCTGACTGCAACGGGCAATATGTCTCTGTGTGGATTAAAAAAAGAGTGTCTGATATCA ....

Now i want to find entropy for each pattern in this genome.

Second question is hot to interpret that values?

• 0 views • link
written by markic • markic

1 answer

For shannon entropy, see the first answer to both these threads:

https://biology.stackexchange.com/questions/64368/how-to-determine-the-height-bits-in-a-sequence-logo
and
Shannon entropy of a DNA motif?

Presumably, you have a motif (pattern) in a position weight matrix format? The motif has it's own entropy, regardless of any genome; it's just a measure of how much information is encoded in a motif.

Motif logo

Note the "bits" on the left of the logo; that's your information.

Or were you thinking of something different relative to a genome? E.g. enrichment of the motif in a genome.

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written by mbelmadani mbelmadani

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