MMseqs2

Databases

Mounted at /db/<name>/<name>:

Example job

Upload a FASTA such as example.fasta and run:

mmseqs createdb /inputs/example.fasta edb
mmseqs search edb /db/pdb/pdb res1 tmp -a
mmseqs result2msa edb /db/pdb/pdb res1 /outputs/ex_pdb.a3m --msa-format-mode 5

Outputs arrive under /outputs; adjust the database path or output filename as needed.

UniRef30 A3M for predictors

mmseqs createdb /inputs/target.fasta queryDB
mmseqs search queryDB /db/uniref30_2302/uniref30_2302 resultDB tmp -a -s 7.5
mmseqs result2msa queryDB /db/uniref30_2302/uniref30_2302 resultDB /outputs/target.a3m --msa-format-mode 5

When feeding result2msa output into parsers that expect strict text A3M, such as Boltz custom MSA input, check for and strip any trailing NUL byte.