Answers.Body: <p>I think MEME is a good tool for your purpose, but there are others as well. I can think of <a href="http://www.ebi.ac.uk/interpro/interproscan.html" rel="nofollow noreferrer">InterProScan</a> for example (although I am not sure if it is really <em>de novo</em>). <a href="https://molbiol-tools.ca/Motifs.htm" rel="nofollow noreferrer">Here</a> a summary of available tools.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-12-04T08:53:41.757Z
Answers.LastActivityDate: 2018-12-04T08:53:41.757Z
Answers.UserDisplayName: benn
Body: <p>I am trying to build a features matrix to be used for Random Forest based classification. I'd like to add, as features, short motifs which are common to all the protein sequences belonging to a specific gene family.</p>
  
  <p>I tried to use MEME but I'd like to know if there are also other good tools (online or command line). Keep in mind I have more than 10.000 sequences and that I prefer short motifs (3/4 aa long).</p>
  
Tags: <proteins><sequence-analysis><motifs><machine-learning>
Title: De novo motif discovery in protein sequences
ThreadText: # De novo motif discovery in protein sequences
  
  (Asked by: username_0 on 2018-12-03)
  
  I am trying to build a features matrix to be used for Random Forest based classification. I'd like to add, as features, short motifs which are common to all the protein sequences belonging to a specific gene family.
  
  I tried to use MEME but I'd like to know if there are also other good tools (online or command line). Keep in mind I have more than 10.000 sequences and that I prefer short motifs (3/4 aa long).
  
  **Tags:** proteins, sequence-analysis, motifs, machine-learning
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2018-12-04. Score: 3
  
  I think MEME is a good tool for your purpose, but there are others as well. I can think of [InterProScan](http://www.ebi.ac.uk/interpro/interproscan.html) for example (although I am not sure if it is really *de novo*). [Here](https://molbiol-tools.ca/Motifs.htm) a summary of available tools.
  
  
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