text: user2862: 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).
  
  user939: I think MEME is a good tool for your purpose, but there are others as well. I can think of InterProScan for example (although I am not sure if it is really de novo). Here a summary of available tools.
  
original_text: 2862: <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>
   939: <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>
  