get_sequences_from_database

biotite.application_v2.mmseqs.get_sequences_from_database(app: MMseqsLikeApp, sequence_db: SequenceDatabase[Any] | ProfileDatabase[Any], as_3di: bool = False) → dict[str, str]

Extract the sequences from a database.

Parameters:

appMMseqsApp or FoldseekApp

The application to use.

sequence_dbSequenceDatabase or ProfileDatabase

The database to read. For a profile database, the representative sequence of each profile is returned, which is the query sequence for profiles created from MSAs. Profile databases are only supported by MMseqsApp.

as_3dibool, optional

If true, extract Foldseek 3Di instead of amino-acid sequences.

Returns:

sequencesdict of str to str

Sequence identifiers mapped to sequences.