Answers.Body: <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>
  
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Answers.CreationDate: 2020-10-25T12:02:50.460Z
Answers.LastActivityDate: 2020-10-25T12:02:50.460Z
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Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2020-10-23T14:13:07.457Z
Comments.Text: Great question! +1
Comments.UserDisplayName: M__
Tags: <python><phylogenetics><features>
Title: Are there computational tools to extract features of DNA sequences?
ThreadText: # Are there computational tools to extract features of DNA sequences?
  
  (Asked by: username_0 on 2020-10-22)
  
  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](https://github.com/mrzResearchArena/PyFeat/blob/master/Codes/generateFeatures.py) script from the [PyFeat](https://github.com/mrzResearchArena/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](https://huggingface.co/transformers/) models for DNA sequences.
  
  ---
  
  ***Edit***:
  In addition, you can use [DeepHF's feature utils](https://github.com/crispr-il/DeepHF/blob/d05444e6fa209e734dabc8defc853585afdffe5b/DeepHF/scripts/feature_util.py), which can be accessed and consumed as seen [here](https://github.com/crispr-il/DeepHF/blob/d05444e6fa209e734dabc8defc853585afdffe5b/DeepHF/scripts/preprocess.py#L133).
  
  **Tags:** python, phylogenetics, features
  
  > **Comments:**
  > **username_1**: Great question! +1  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2020-10-25. Score: 2
  
  If you want to do this with biopython, the [SeqUtils](https://biopython.org/docs/1.75/api/Bio.SeqUtils.html) package could be a solution.
  
  
  ---
  
  