sokrypton / sokrypton/ColabFold
Databases used in the mmseq2 search, local version
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- Dominant language
- Jupyter Notebook
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Description
Hello,
I would like to run locally the msa building step of the colab notebook and use the exact same set of databases to do some comparison with other databases.
Is it possible to get access to the set of databases the mmseq2 server is using as well as the version of mmseqs2 and the specific command lines executed on the server?
In the slides you presented (awesome presentation!), you mentioned you are using a 30%id clustered DB built from SMAG, MGNIFY, BFD, and MetaEuk. Do you provide somewhere a downloadable version of the master 30%seq_id db?
Thanks a lot!
Contributor guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
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Research direction
Start by reviewing the Colab notebook and the MMseqs2 server workflow referenced in the issue; no repository file or test is identified. Done would mean establishing whether the server's database set, MMseqs2 version, command lines, and 30% identity database are documented or downloadable.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics, databases
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100