sokrypton / sokrypton/ColabFold
When downloading database for local MSA, what is the format of the database folder?
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Description
Is it normal for the finished database (after mmseqs tsv2exprofiledb and mmseqs createindex) to consist of:
colabfold_envdb_202108.tsv
colabfold_envdb_202108_aln.tsv
colabfold_envdb_202108_db.0-63 (64 files)
colabfold_envdb_202108_db.dbtype
colabfold_envdb_202108.idx.1-4 (4 files)
colabfold_envdb_202108_db.idx.dbtype
colabfold_envdb_202108_db.index
colabfold_envdb_202108_db_aln.0-63 (64 files)
colabfold_envdb_202108_db_aln.dbtype
colabfold_envdb_202108_db_aln.index
colabfold_envdb_202108_db_h
colabfold_envdb_202108_db_h.dbtype
colabfold_envdb_202108_db_h.index
colabfold_envdb_202108_db_seq.0-63 (64 files)
colabfold_envdb_202108_db_seq.dbtype
colabfold_envdb_202108_db_seq.index
colabfold_envdb_202108_db_seq_h
colabfold_envdb_202108_db_seq_h.dbtype
colabfold_envdb_202108_db_seq_h.index
colabfold_envdb_202108_db_h.tsv
colabfold_envdb_202108_seq.tsv
and then a similar set of files all for uniref30_2103
or is something going wrong during the mmseqs command?
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 issue's listed outputs and the mmseqs tsv2exprofiledb and createindex commands. Check mmseqs documentation or a reproducible local MSA database build to determine whether the ColabFold and uniref30 file sets are expected. Done means confirming the folder layout or identifying a command problem and documenting the expected result.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics, databases
- Issue type
- Documentation
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100