text: user734: 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.
  
  user3360: If you want to do this with biopython, the SeqUtils package could be a solution.
  
original_text: 734: <p>I am looking for tools to extract features from short DNA sequences. For example, entropy, complexity, GC-content, etc.</p>
  <p>I have found the <a href="https://github.com/mrzResearchArena/PyFeat/blob/master/Codes/generateFeatures.py" rel="nofollow noreferrer">generateFeatures.py</a> script from the <a href="https://github.com/mrzResearchArena/PyFeat/" rel="nofollow noreferrer">PyFeat</a> repo, but is there love a more widely used source code or a standard way to extract features from sequences biopython or similar?</p>
  <p>Also, I think that since there are <span class="math-container">$2N$</span> encoded bits in a sequence of <span class="math-container">$N$</span> nucleotides, we have <strong>at most</strong> <span class="math-container">$2N$</span> independent features that could be extracted.</p>
  <hr />
  <p>In addition, I am curios if there are any <a href="https://huggingface.co/transformers/" rel="nofollow noreferrer">transformers</a> models for DNA sequences.</p>
  <hr />
  <p><em><strong>Edit</strong></em>:
  In addition, you can use <a href="https://github.com/crispr-il/DeepHF/blob/d05444e6fa209e734dabc8defc853585afdffe5b/DeepHF/scripts/feature_util.py" rel="nofollow noreferrer">DeepHF's feature utils</a>, which can be accessed and consumed as seen <a href="https://github.com/crispr-il/DeepHF/blob/d05444e6fa209e734dabc8defc853585afdffe5b/DeepHF/scripts/preprocess.py#L133" rel="nofollow noreferrer">here</a>.</p>
   3360: <p>If you want to do this with biopython, the <a href="https://biopython.org/docs/1.75/api/Bio.SeqUtils.html" rel="nofollow noreferrer">SeqUtils</a> package could be a solution.</p>
  