Answers.Body: <p>I might be missing something, but this is basically BLASTP. Is there a reason that you don't want to use the standard alignment based homology searches against a database?</p>
  <p>You will of course want to <a href="https://www.biostars.org/p/47203/" rel="nofollow noreferrer">adjust word size and E value thresholds</a> accordingly for what is presumably a short input. They have a few substitution matrix options, though I'm not sure that you can be fully custom without <a href="https://www.biostars.org/p/502/#26553" rel="nofollow noreferrer">modifying the source code</a>.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2024-12-28T20:30:20.803Z
Answers.LastActivityDate: 2024-12-28T20:30:20.803Z
Answers.UserDisplayName: Maximilian Press
Body: <p>Currently I'm working with Foldseek and its 3Di-based alphabet, and I wanted to search and isolate proteins within my database that contained a similar k-mer to an unique k-mer I had found. I do not see any present way to do this through foldseek, having looked through the github and wiki extensively.</p>
  <p>I was wondering if there are any existing bioinformatics tools (and ones that don't specifically focus on nucleotide sequences) that can search for a specific k-mer along a database? Additionally, do any of these tools work with a substitution matrix opposed to direct sequence coverage? If so, any way to customize the substitution matrix to the specific sequence language I'm using?</p>
  <p>Thanks</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2024-12-23T15:17:21.790Z
Comments.Text: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.
Comments.UserDisplayName: Community
Tags: <sequence-analysis><k-mer><sequence-homology>
Title: Existing tools for specific k-mer-based searches
ThreadText: # Existing tools for specific k-mer-based searches
  
  (Asked by: username_0 on 2024-12-23)
  
  Currently I'm working with Foldseek and its 3Di-based alphabet, and I wanted to search and isolate proteins within my database that contained a similar k-mer to an unique k-mer I had found. I do not see any present way to do this through foldseek, having looked through the github and wiki extensively.
  
  I was wondering if there are any existing bioinformatics tools (and ones that don't specifically focus on nucleotide sequences) that can search for a specific k-mer along a database? Additionally, do any of these tools work with a substitution matrix opposed to direct sequence coverage? If so, any way to customize the substitution matrix to the specific sequence language I'm using?
  
  Thanks
  
  **Tags:** sequence-analysis, k-mer, sequence-homology
  
  > **Comments:**
  > **username_1**: Please clarify your specific problem or provide additional details to highlight exactly what you need. As it's currently written, it's hard to tell exactly what you're asking.  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_2 on 2024-12-28. Score: 1
  
  I might be missing something, but this is basically BLASTP. Is there a reason that you don't want to use the standard alignment based homology searches against a database?
  
  You will of course want to [adjust word size and E value thresholds](https://www.biostars.org/p/47203/) accordingly for what is presumably a short input. They have a few substitution matrix options, though I'm not sure that you can be fully custom without [modifying the source code](https://www.biostars.org/p/502/#26553).
  
  
  ---
  
  