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I am looking for tools to extract features from short DNA sequences. For example, entropy, complexity, GC-content, etc.

I have found the generateFeatures.py script from the PyFeat repo, but is there love a more widely used source code or a standard way to extract features from sequences biopython or similar?

Also, I think that since there are $2N$ encoded bits in a sequence of $N$ nucleotides, we have at most $2N$ independent features that could be extracted.

In addition, I am curios if there are any transformers models for DNA sequences.

Edit: In addition, you can use DeepHF's feature utils, which can be accessed and consumed as seen here.

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    $\begingroup$ Great question! +1 $\endgroup$
    – M__ ♦
    Oct 23, 2020 at 14:13

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If you want to do this with biopython, the SeqUtils package could be a solution.

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