get_alignments

biotite.application_v2.mmseqs.get_alignments(app: ~biotite.application_v2.mmseqs.util.T, alignment_db: ~biotite.application_v2.mmseqs.AlignmentDatabase[~biotite.application_v2.mmseqs.util.T], sequence_type: type[~biotite.sequence.Sequence] = <class 'biotite.sequence.ProteinSequence'>) → dict[tuple[str, str], Alignment]

Reconstruct Biotite alignments from an alignment database.

Parameters:

appMMseqsApp or FoldseekApp

The application to use.

alignment_dbAlignmentDatabase

The alignment database to read. The search that created alignment_db must enable backtracing with a=True.

sequence_typetype of Sequence, optional

The type the aligned sequences are parsed into. biotite.structure.alphabet.I3DSequence reconstructs the alignments from the 3Di sequences of a Foldseek database instead of from the amino acid sequences.

Returns:

alignmentsdict

(query_id, target_id) pairs mapped to alignments. Entries are ordered by increasing E-value.

Notes

The identifiers are the ones the application parsed from the FASTA headers, e.g. the accession for UniProt-style headers, and thus may differ from the identifiers given to get_sequences_from_database().

Gallery

Homology search and multiple sequence alignment

Homology search and multiple sequence alignment

Mutual information as measure for coevolution of residues

Mutual information as measure for coevolution of residues