get_msa_from_database

biotite.application_v2.mmseqs.get_msa_from_database(app: ~biotite.application_v2.mmseqs.app.MMseqsApp, msa_db: ~biotite.application_v2.mmseqs.MSADatabase[~biotite.application_v2.mmseqs.app.MMseqsApp], sequence_type: type[~biotite.sequence.Sequence] = <class 'biotite.sequence.ProteinSequence'>) → dict[str, list[Alignment]]

Extract the MSAs from an MSA database.

Parameters:

appMMseqsApp

The application to use.

msa_dbMSADatabase

The database to read. Its entries must be in A3M format, i.e. the first sequence of each MSA must be an ungapped query.

sequence_typetype of Sequence, optional

The type the aligned sequences are parsed into.

Returns:

msadict (str -> list of Alignment)

MSA identifiers mapped to the respective MSA, given as pairwise alignments of its query to each of its homologs.

See also

create_database_from_msa

The inverse operation.

Notes

The identifier of each MSA is taken from the first sequence of the MSA, as an MSA database does not store identifiers separately.