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?

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First steps

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  3. Fork the repository and make your change on a branch.
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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

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