sokrypton / sokrypton/ColabFold
local MSAs different to ipynb-MSAs
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Description
Expected Behavior
MSAs generated locally and on the ipynb should be identical
Current Behavior
local MSA coverage
ipynb MSA coverage
Steps to Reproduce (for bugs)
I am running the MSA prediction as indicated in the readme without any options. I use the latest commit of mmseqs2 and the database hosted here https://colabfold.mmseqs.com/.
Are there any special settings that need to be applied to replicate the default colabfold behavior?
Thank you,
Dominik
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.
- Open a pull request that references the issue number.
Research direction
Start with the README instructions for local MSA prediction and compare them with the ipynb workflow. Reproduce both runs using the latest mmseqs2 commit and the hosted database specified in the report, then identify the differing settings or inputs. Done means the local and ipynb MSAs have matching coverage, or the required settings are documented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100