sokrypton / sokrypton/ColabFold
Custom MSA in batch mode (AlphaFold2_batch.ipynb)
Nobody has claimed this yet.
- Dominant language
- Jupyter Notebook
- Stars
- 2.9k
- Forks
- 747
- PR merge metrics
- No merged PRs in 30d
Description
Hi i was trying to use custom MSA(s) in batch mode (AlphaFold2_batch.ipynb). But there is no upload option. Does it work if the .a3m files are provided in the input directory as the first sequence should be treated as the query?
And also: is it possible to reduce the clustered:extra sequences cap / max_msa of a custom uploaded msa ?
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 by reading AlphaFold2_batch.ipynb and tracing how the input directory and multiple-sequence alignments are handled. Determine whether .a3m files are currently accepted and where clustered and extra sequence limits are applied. Done means the supported custom-MSA workflow and max_msa behavior are implemented or clearly documented.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- jupyter-notebook
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100