text: user15741: I need a tool or a function I can use in my code (R, or Python) that I can cross reference a MOTIF against known MOTIFS, a function that will take as input a MOTIF (a probability weight matrix, PWM which is a 4 by m matrix for an m-length motif) and spit out the closest -n- known motif(s). Is there such a function/tool or something close to it? Thanks much.
  
  user73: Answer from @m, converted from comment:
  Hi @ZebraFish Motifs package Biopython
  https://biopython.org/docs/1.76/api/Bio.motifs.html
  
  user1692: A popular tool for doing this is tomtom, part of the meme package.
  You can try it via interactive web form here.
  Once installed locally it can be run via command line
  Additionally, it is available in the Bioconductor package memes as explained in Motif Comparison using TomTom
  
original_text: 15741: <p>I need a tool or a function I can use in my code (R, or Python) that I can cross reference a MOTIF against known MOTIFS, a function that will take as input a MOTIF (a probability weight matrix, PWM which is a 4 by m matrix for an m-length motif) and spit out the closest -n- known motif(s). Is there such a function/tool or something close to it? Thanks much.</p>
   73: <p><em>Answer from @m, converted from comment:</em></p>
  <p>Hi @ZebraFish Motifs package Biopython</p>
  <p><a href="https://biopython.org/docs/1.76/api/Bio.motifs.html" rel="nofollow noreferrer">https://biopython.org/docs/1.76/api/Bio.motifs.html</a></p>
   1692: <p>A popular tool for doing this is tomtom, part of the meme package.</p>
  <p>You can try it via interactive web form <a href="https://meme-suite.org/meme/tools/tomtom" rel="nofollow noreferrer">here</a>.</p>
  <p>Once installed locally it can be <a href="https://meme-suite.org/meme/doc/tomtom.html?man_type=web" rel="nofollow noreferrer">run via command line</a></p>
  <p>Additionally, it is available in the Bioconductor package <code>memes</code> as explained in <a href="https://snystrom.github.io/memes-manual/articles/core_tomtom.html" rel="nofollow noreferrer">Motif Comparison using TomTom</a></p>
  