sokrypton / sokrypton/ColabFold
k-mers and minimum recommended sequence length
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Description
Hi!
I am trying to learn what is the minimum amino acid sequence length to run a ColabFold prediction using MMSeq2 for the MSA. I have seen responses that say that MMseqs2 uses k-mer of 6, therefore the minimum length of a hit can be 13 for the gapped and 12 for the ungapped. Also, I've seen responses saying that MMseq2 struggles with sequences <20 aminoacids.
Could you please be so kind an clear out this for me and let me know what are the steps/settings/arguments that specify those limits? For example, does ColabFold when using MMseq2 to run MSAs on the server / locally after constructing the databases use a default k-mer and what is the default k-mer? I am sorry if this question is trivial, but I was not able to find a clear specification.
Are there any tests showing performance over length or it based on experience?
Thank you very much!
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Research direction
The issue names no files, tests, or entry points. Begin by locating ColabFold's MMseqs2 configuration and comparing its defaults with MMseqs2 documentation; done means documenting the relevant k-mer, sequence-length limits, settings, and any available performance evidence.
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Assessment
- Domain
- bioinformatics
- Issue type
- Documentation
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100