<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>

CC BY-SA 4.0
2024-12-28T20:30:20.803Z
2024-12-28T20:30:20.803Z
Maximilian Press
<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>

CC BY-SA 4.0
2024-12-23T15:17:21.790Z
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.
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<sequence-analysis><k-mer><sequence-homology>
Existing tools for specific k-mer-based searches
# 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.  

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## 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).


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