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  • biotite
    • File
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  • biotite.application
    • Application
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  • biotite.application.autodock
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  • biotite.application.blast
    • BlastAlignment
    • BlastWebApp
  • biotite.application.clustalo
    • ClustalOmegaApp
  • biotite.application.dssp
    • DsspApp
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    • TantanApp
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    • RNAalifoldApp
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  • biotite.database
    • RequestError
  • biotite.database.afdb
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  • biotite.database.entrez
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  • biotite.database.pubchem
    • Query
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  • biotite.database.rcsb
    • Query
    • SingleQuery
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  • biotite.database.uniprot
    • CompositeQuery
    • Query
    • SimpleQuery
    • fetch
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  • biotite.interface
    • LossyConversionWarning
  • biotite.interface.openmm
    • from_context
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    • to_topology
  • biotite.interface.pymol
    • launch_pymol
    • launch_interactive_pymol
    • reset
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    • DuplicatePyMOLError
    • PyMOLObject
    • to_model
    • from_model
    • draw_cgo
    • get_cylinder_cgo
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    • get_point_cgo
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    • get_multiline_cgo
    • draw_arrows
    • draw_box
    • show
    • play
    • ModifiedObjectError
    • NonexistentObjectError
    • RenderError
    • TimeoutError
  • biotite.interface.rdkit
    • from_mol
    • to_mol
  • biotite.sequence
    • Sequence
    • NucleotideSequence
    • ProteinSequence
    • GeneralSequence
    • Alphabet
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    • common_alphabet
    • Feature
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    • find_subsequence
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    • SequenceProfile
  • biotite.sequence.align
    • SubstitutionMatrix
    • align_ungapped
    • align_optimal
    • align_local_ungapped
    • align_local_gapped
    • align_banded
    • align_multiple
    • Alignment
    • get_codes
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    • get_sequence_identity
    • get_pairwise_sequence_identity
    • score
    • KmerAlphabet
    • KmerTable
    • BucketKmerTable
    • SimilarityRule
    • ScoreThresholdRule
    • bucket_number
    • MinimizerSelector
    • SyncmerSelector
    • CachedSyncmerSelector
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    • Permutation
    • RandomPermutation
    • FrequencyPermutation
    • CigarOp
    • read_alignment_from_cigar
    • write_alignment_to_cigar
    • EValueEstimator
    • find_terminal_gaps
    • remove_gaps
    • remove_terminal_gaps
  • biotite.sequence.graphics
    • plot_feature_map
    • plot_sequence_logo
    • plot_alignment
    • plot_alignment_similarity_based
    • plot_alignment_type_based
    • plot_dendrogram
    • SymbolPlotter
    • LetterPlotter
    • LetterSimilarityPlotter
    • LetterTypePlotter
    • FeaturePlotter
    • CodingPlotter
    • PromoterPlotter
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    • RBSPlotter
    • MiscFeaturePlotter
    • load_color_scheme
    • get_color_scheme
    • list_color_scheme_names
    • ArrayPlotter
    • plot_alignment_array
    • plot_plasmid_map
  • biotite.sequence.io
    • load_sequence
    • load_sequences
    • save_sequence
    • save_sequences
  • biotite.sequence.io.fasta
    • FastaFile
    • get_alignment
    • get_sequence
    • get_sequences
    • set_alignment
    • set_sequence
    • set_sequences
  • biotite.sequence.io.fastq
    • FastqFile
    • get_sequence
    • get_sequences
    • set_sequence
    • set_sequences
  • biotite.sequence.io.genbank
    • GenBankFile
    • MultiFile
    • get_accession
    • get_annotated_sequence
    • get_annotation
    • get_db_link
    • get_definition
    • get_gi
    • get_locus
    • get_raw_sequence
    • get_sequence
    • get_source
    • get_version
    • set_annotated_sequence
    • set_annotation
    • set_locus
    • set_sequence
  • biotite.sequence.io.gff
    • GFFFile
    • get_annotation
    • set_annotation
  • biotite.sequence.phylo
    • Tree
    • TreeNode
    • TreeError
    • as_binary
    • upgma
    • neighbor_joining
  • biotite.structure
    • Atom
    • AtomArray
    • AtomArrayStack
    • concatenate
    • array
    • stack
    • repeat
    • from_template
    • vectors_from_unitcell
    • unitcell_from_vectors
    • box_volume
    • repeat_box
    • repeat_box_coord
    • move_inside_box
    • remove_pbc
    • remove_pbc_from_coord
    • coord_to_fraction
    • fraction_to_coord
    • is_orthogonal
    • BondList
    • BondType
    • connect_via_residue_names
    • connect_via_distances
    • find_connected
    • find_rotatable_bonds
    • displacement
    • index_displacement
    • distance
    • index_distance
    • angle
    • index_angle
    • dihedral
    • index_dihedral
    • centroid
    • mass_center
    • gyration_radius
    • rdf
    • translate
    • rotate
    • rotate_centered
    • rotate_about_axis
    • align_vectors
    • orient_principal_components
    • superimpose
    • superimpose_without_outliers
    • superimpose_homologs
    • superimpose_structural_homologs
    • AffineTransformation
    • filter_canonical_nucleotides
    • filter_nucleotides
    • filter_canonical_amino_acids
    • filter_amino_acids
    • filter_carbohydrates
    • filter_peptide_backbone
    • filter_phosphate_backbone
    • filter_linear_bond_continuity
    • filter_polymer
    • filter_solvent
    • filter_monoatomic_ions
    • filter_intersection
    • filter_first_altloc
    • filter_highest_occupancy_altloc
    • check_atom_id_continuity
    • check_res_id_continuity
    • check_backbone_continuity
    • check_duplicate_atoms
    • check_linear_continuity
    • create_continuous_res_ids
    • infer_elements
    • create_atom_names
    • get_residue_starts
    • get_residues
    • apply_residue_wise
    • spread_residue_wise
    • get_residue_masks
    • get_residue_starts_for
    • get_residue_positions
    • get_residue_count
    • residue_iter
    • get_chain_starts
    • apply_chain_wise
    • spread_chain_wise
    • get_chain_masks
    • get_chain_starts_for
    • get_chain_positions
    • get_chains
    • get_chain_count
    • chain_iter
    • get_molecule_indices
    • get_molecule_masks
    • molecule_iter
    • average
    • rmsd
    • rmspd
    • rmsf
    • lddt
    • tm_score
    • sasa
    • hbond
    • hbond_frequency
    • partial_charges
    • density
    • dihedral_backbone
    • annotate_sse
    • Edge
    • GlycosidicBond
    • map_nucleotide
    • base_pairs
    • base_stacking
    • pseudoknots
    • base_pairs_edge
    • base_pairs_glycosidic_bond
    • dot_bracket
    • dot_bracket_from_structure
    • base_pairs_from_dot_bracket
    • find_aromatic_rings
    • find_stacking_interactions
    • PiStacking
    • BadStructureError
    • CellList
    • IncompleteStructureWarning
    • UnexpectedStructureWarning
    • coord
    • to_sequence
  • biotite.structure.alphabet
    • I3DSequence
    • ProteinBlocksSequence
    • to_3di
    • to_protein_blocks
  • biotite.structure.graphics
    • plot_atoms
    • plot_ball_and_stick_model
    • plot_nucleotide_secondary_structure
  • biotite.structure.info
    • residue
    • bond_type
    • bonds_in_residue
    • amino_acid_names
    • nucleotide_names
    • carbohydrate_names
    • vdw_radius_single
    • vdw_radius_protor
    • get_ccd
    • get_from_ccd
    • set_ccd_path
    • all_residues
    • full_name
    • link_type
    • mass
    • one_letter_code
    • standardize_order
  • biotite.structure.io
    • TrajectoryFile
    • load_structure
    • save_structure
  • biotite.structure.io.dcd
    • DCDFile
  • biotite.structure.io.gro
    • GROFile
  • biotite.structure.io.mol
    • Header
    • MOLFile
    • Metadata
    • SDFile
    • SDRecord
    • get_structure
    • set_structure
  • biotite.structure.io.netcdf
    • NetCDFFile
  • biotite.structure.io.pdb
    • PDBFile
    • get_assembly
    • get_model_count
    • get_structure
    • get_symmetry_mates
    • list_assemblies
    • set_structure
  • biotite.structure.io.pdbqt
    • PDBQTFile
    • get_structure
    • set_structure
  • biotite.structure.io.pdbx
    • get_sequence
    • get_model_count
    • get_structure
    • set_structure
    • get_component
    • set_component
    • list_assemblies
    • get_assembly
    • get_sse
    • CIFFile
    • CIFBlock
    • CIFCategory
    • CIFColumn
    • CIFData
    • BinaryCIFFile
    • BinaryCIFBlock
    • BinaryCIFCategory
    • BinaryCIFColumn
    • BinaryCIFData
    • ByteArrayEncoding
    • FixedPointEncoding
    • IntervalQuantizationEncoding
    • RunLengthEncoding
    • DeltaEncoding
    • IntegerPackingEncoding
    • StringArrayEncoding
    • TypeCode
    • MaskValue
    • compress
  • biotite.structure.io.trr
    • TRRFile
  • biotite.structure.io.xtc
    • XTCFile
  • API Reference
  • biotite.application.blast

BlastWebApp#

biotite.application.blast.BlastWebApp[source]#

alias of MockedBlastApp

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
On this page
  • BlastWebApp
  • Gallery
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