Index

A

a() (in module pydna.threading_timer_decorator_exit) accession (pydna.seqrecord.SeqRecord property) add_colors_to_features_for_ape() (pydna.seqrecord.SeqRecord method) add_dseqrecord() (pydna.opencloning_models.CloningStrategy method) add_edges_from_match() (pydna.assembly2.Assembly method) add_feature() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) (pydna.seqrecord.SeqRecord method) add_primer() (pydna.opencloning_models.CloningStrategy method) add_primer_features (pydna.opencloning_models.PCRSource attribute) add_to_history_graph() (pydna.opencloning_models.Source method) addgene_sequence_type (pydna.opencloning_models.AddgeneIdSource attribute) AddgeneIdSource (class in pydna.opencloning_models) Amplicon (class in pydna.amplicon) amplicon_tuple (class in pydna.primer_screen) Anneal (class in pydna.all) (class in pydna.amplify) anneal_from_left() (in module pydna.utils) anneal_strands() (in module pydna.alphabet) annotate_gateway_sites() (in module pydna.gateway) annotate_loxP_sites() (in module pydna.cre_lox) annotate_primer_binding_sites() (in module pydna.assembly2) annotation_report (pydna.opencloning_models.AnnotationSource attribute) annotation_tool (pydna.opencloning_models.AnnotationSource attribute) annotation_tool_version (pydna.opencloning_models.AnnotationSource attribute) annotations (pydna.dseqrecord.Dseqrecord attribute) AnnotationSource (class in pydna.opencloning_models)

apply_cut() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) assemble() (in module pydna.assembly2) assemble_circular() (pydna.all.Assembly method) (pydna.assembly.Assembly method) (pydna.assembly2.Assembly method) assemble_insertion() (pydna.assembly2.Assembly method) assemble_linear() (pydna.all.Assembly method) (pydna.assembly.Assembly method) (pydna.assembly2.Assembly method) (pydna.assembly2.PCRAssembly method) Assembly (class in pydna.all) (class in pydna.assembly) (class in pydna.assembly2) assembly2str() (in module pydna.assembly2) assembly2str_tuple() (in module pydna.assembly2) assembly_accession (pydna.opencloning_models.GenomeCoordinatesSource attribute) assembly_fragments() (in module pydna.all) (in module pydna.design) assembly_has_mismatches() (in module pydna.assembly2) assembly_is_circular() (in module pydna.assembly2) assembly_is_multi_site() (in module pydna.assembly2) assembly_is_valid() (pydna.assembly2.Assembly class method) assembly_uses_only_adjacent_edges() (pydna.assembly2.Assembly method) AssemblyFragment (class in pydna.opencloning_models) AssemblySource (class in pydna.opencloning_models)

B

b() (in module pydna.threading_timer_decorator_exit) back_transcribe() (pydna.seq.ProteinSeq method)

BenchlingUrlSource (class in pydna.opencloning_models) blunt_overlap() (in module pydna.assembly2)

C

c() (in module pydna.threading_timer_decorator_exit) cai() (in module pydna.utils) (pydna.seq.Seq method) (pydna.seqrecord.ProteinSeqRecord method) (pydna.seqrecord.SeqRecord method) callback() (in module pydna.primer_screen) cas9 (class in pydna.crispr) cast_to_ds() (pydna.all.Dseq method) (pydna.dseq.Dseq method) cast_to_ds_left() (pydna.all.Dseq method) (pydna.dseq.Dseq method) cast_to_ds_right() (pydna.all.Dseq method) (pydna.dseq.Dseq method) cdquit() (in module pydna.threading_timer_decorator_exit) circular (pydna.all.Dseqrecord property) (pydna.dseqrecord.Dseqrecord property) (pydna.opencloning_models.AssemblySource attribute) circular_assembly_fragments() (in module pydna.design) circular_permutation_min_abs() (in module pydna.assembly2) CircularBytes (class in pydna.dseq) CloningStrategy (class in pydna.opencloning_models) closest_diff() (in module pydna.primer_screen) combine_algorithms() (in module pydna.assembly2) comment() (pydna.seqrecord.SeqRecord method) common_function_assembly_products() (in module pydna.assembly2) common_function_excision_products() (in module pydna.assembly2) common_function_integration_products() (in module pydna.assembly2) common_handle_insertion_fragments() (in module pydna.assembly2) common_sub_strings() (in module pydna.assembly2) (in module pydna.common_sub_strings) complement() (in module pydna.utils) (pydna.seq.ProteinSeq method) complement_rna() (pydna.seq.ProteinSeq method)

compute_regex_site() (in module pydna.sequence_regex) concat_dict() (in module pydna.genbankfixer) ConfiguredBaseModel (class in pydna.opencloning_models) Contig (class in pydna.contig) coordinates (pydna.opencloning_models.GenomeCoordinatesSource attribute) (pydna.opencloning_models.NCBISequenceSource attribute) copy() (pydna.seqrecord.SeqRecord method) copy_fasta_to_clipboard() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) copy_gb_to_clipboard() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) countdown() (in module pydna.threading_timer_decorator_exit) cre_lox_excision() (in module pydna.assembly2) cre_lox_integration() (in module pydna.assembly2) cre_loxP_overlap() (in module pydna.cre_lox) create_location() (in module pydna.utils) CreLoxRecombinationSource (class in pydna.opencloning_models) crick (pydna.all.Dseq property) (pydna.dseq.Dseq property) crispr_integration() (in module pydna.assembly2) CRISPRSource (class in pydna.opencloning_models) cut() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) cutaround() (pydna.dseq.CircularBytes method) cuts_overlap() (in module pydna.utils) cutsite_is_valid() (pydna.all.Dseq method) (pydna.dseq.Dseq method) cutters() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method)

D

d() (in module pydna.threading_timer_decorator_exit) database_id (pydna.opencloning_models.DatabaseSource attribute) DatabaseSource (class in pydna.opencloning_models) datefunction() (pydna.seqrecord.SeqRecord method) dbd_program() (in module pydna.tm) (pydna.amplicon.Amplicon method) dbxrefs (pydna.dseqrecord.Dseqrecord attribute) definition (pydna.seqrecord.SeqRecord property) detailed_figure() (pydna.contig.Contig method)

diff_primer_pairs() (in module pydna.primer_screen) diff_primer_triplets() (in module pydna.primer_screen) dsbreaks() (in module pydna.alphabet) Dseq (class in pydna.all) (class in pydna.dseq) DseqParts (class in pydna.alphabet) Dseqrecord (class in pydna.all) (class in pydna.dseqrecord) dseqrecord_finditer() (in module pydna.sequence_regex) dump() (pydna.seqrecord.SeqRecord method)

E

edge_representation2subfragment_representation() (in module pydna.assembly2) embl_gb_fasta() (in module pydna.parsers) ends_from_cutsite() (in module pydna.assembly2) eq() (in module pydna.all) (in module pydna.utils) EuroscarfSource (class in pydna.opencloning_models) exit_after() (in module pydna.threading_timer_decorator_exit) exo1_end() (pydna.all.Dseq method) (pydna.dseq.Dseq method) exo1_front() (pydna.all.Dseq method) (pydna.dseq.Dseq method)

expand_iupac_to_dna() (in module pydna.primer_screen) express() (in module pydna.utils) (pydna.seq.Seq method) (pydna.seqrecord.ProteinSeqRecord method) (pydna.seqrecord.SeqRecord method) extract_feature() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) (pydna.seqrecord.SeqRecord method) extract_from_text() (in module pydna.parsers) extract_subfragment() (in module pydna.assembly2)

F

FakeSeq (class in pydna.fakeseq) field_validator() (pydna.opencloning_models.SequenceLocationStr class method) figure() (pydna.all.Dseqrecord method) (pydna.amplicon.Amplicon method) (pydna.contig.Contig method) (pydna.dseqrecord.Dseqrecord method) figure_mpl() (pydna.contig.Contig method) file_name (pydna.opencloning_models.UploadedFileSource attribute) fill_in() (pydna.all.Dseq method) (pydna.dseq.Dseq method) filter_linear_subassemblies() (in module pydna.assembly2) find() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.CircularBytes method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) find_aa() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) find_aminoacids() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) find_gateway_sites() (in module pydna.gateway) find_loxP_sites() (in module pydna.cre_lox) five_prime_end() (pydna.all.Dseq method) (pydna.dseq.Dseq method) flanking_primer_pairs() (in module pydna.primer_screen) flatten() (in module pydna.utils) footprint (pydna.primer.Primer property) format() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) format_assembly_edge() (pydna.assembly2.Assembly method) format_insertion_assembly() (pydna.assembly2.Assembly method)

format_insertion_assembly_edge_case() (pydna.assembly2.Assembly method) forward_primers (pydna.all.Anneal attribute) (pydna.amplify.Anneal attribute) forward_primers() (in module pydna.primer_screen) fp (pydna.primer_screen.amplicon_tuple attribute) (pydna.primer_screen.primer_tuple attribute) fposition (pydna.primer_screen.amplicon_tuple attribute) from_Bio_SeqRecord() (pydna.seqrecord.SeqRecord class method) from_biopython_location() (pydna.opencloning_models.AssemblyFragment static method) (pydna.opencloning_models.SequenceLocationStr class method) from_dseqrecord() (pydna.opencloning_models.TextFileSequence class method) from_dseqrecords() (pydna.opencloning_models.CloningStrategy class method) from_full_sequence_and_overhangs() (pydna.all.Dseq class method) (pydna.dseq.Dseq class method) from_parent() (pydna.opencloning_models.SequenceCutSource class method) from_primer() (pydna.opencloning_models.PrimerModel class method) from_representation() (pydna.all.Dseq class method) (pydna.dseq.Dseq class method) from_SeqRecord() (pydna.all.Dseqrecord class method) (pydna.amplicon.Amplicon class method) (pydna.contig.Contig class method) (pydna.dseqrecord.Dseqrecord class method) from_start_and_end() (pydna.opencloning_models.SequenceLocationStr class method) from_string() (pydna.all.Dseqrecord class method) (pydna.contig.Contig class method) (pydna.dseqrecord.Dseqrecord class method) from_subfragment_representation() (pydna.opencloning_models.AssemblySource class method) fst3 (pydna.crispr.cas9 attribute) fst5 (pydna.crispr.cas9 attribute) fuse_by_pcr() (in module pydna.fusionpcr) fusion_pcr_assembly() (in module pydna.assembly2)

G

gateway_assembly() (in module pydna.assembly2) gateway_overlap() (in module pydna.gateway) GatewaySource (class in pydna.opencloning_models) gather_overlapping_locations() (in module pydna.assembly2) gbtext_clean() (in module pydna.all) (in module pydna.genbankfixer) gc() (pydna.seq.Seq method) (pydna.seqrecord.ProteinSeqRecord method) (pydna.seqrecord.SeqRecord method) gel() (in module pydna.gel) Genbank (class in pydna.all) (class in pydna.genbank) genbank() (in module pydna.all) (in module pydna.genbank) genbank_accession() (in module pydna.sequence_picker) gene_id (pydna.opencloning_models.GenomeCoordinatesSource attribute) GenomeCoordinatesSource (class in pydna.opencloning_models) get_assembly_subfragments() (in module pydna.assembly2) get_circular_assemblies() (pydna.assembly2.Assembly method) (pydna.assembly2.PCRAssembly method) (pydna.assembly2.SingleFragmentAssembly method) get_cut_parameters() (pydna.all.Dseq method) (pydna.dseq.Dseq method) get_cutsite_pairs() (pydna.all.Dseq method) (pydna.dseq.Dseq method) get_cutsites() (pydna.all.Dseq method) (pydna.dseq.Dseq method)

get_ds_meltsites() (pydna.all.Dseq method) (pydna.dseq.Dseq method) get_env() (in module pydna) get_id() (in module pydna.opencloning_models) get_insertion_assemblies() (pydna.assembly2.Assembly method) (pydna.assembly2.PCRAssembly method) (pydna.assembly2.SingleFragmentAssembly method) get_linear_assemblies() (pydna.assembly2.Assembly method) (pydna.assembly2.PCRAssembly method) (pydna.assembly2.SingleFragmentAssembly method) get_locations_on_fragments() (pydna.assembly2.Assembly method) get_ncbi_format_coordinates() (pydna.opencloning_models.SequenceLocationStr method) get_parts() (in module pydna.alphabet) (pydna.all.Dseq method) (pydna.dseq.Dseq method) get_possible_assembly_number() (pydna.assembly2.Assembly method) get_regex_dict() (in module pydna.cre_lox) get_ss_meltsites() (pydna.all.Dseq method) (pydna.dseq.Dseq method) get_unique_linear_paths() (pydna.assembly2.Assembly method) gibson_assembly() (in module pydna.assembly2) gibson_overlap() (in module pydna.assembly2) GibsonAssemblySource (class in pydna.opencloning_models) golden_gate_assembly() (in module pydna.assembly2) greedy (pydna.opencloning_models.GatewaySource attribute)

H

history() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) history_string() (pydna.opencloning_models.Source method)

homologous_recombination_excision() (in module pydna.assembly2) homologous_recombination_integration() (in module pydna.assembly2) HomologousRecombinationSource (class in pydna.opencloning_models)

I

id_mode() (in module pydna.opencloning_models) identifier_from_string() (in module pydna.utils) IGEMSource (class in pydna.opencloning_models) in_fusion_assembly() (in module pydna.assembly2) in_fusion_overlap() (in module pydna.assembly2) in_vivo_assembly() (in module pydna.assembly2) index_in_file (pydna.opencloning_models.UploadedFileSource attribute) InFusionSource (class in pydna.opencloning_models)

input (pydna.opencloning_models.Source attribute) instability_index() (pydna.seq.ProteinSeq method) interpolator() (in module pydna.gel) InVivoAssemblySource (class in pydna.opencloning_models) is_sublist() (in module pydna.assembly2) isblunt() (pydna.all.Dseq method) (pydna.dseq.Dseq method) isorf() (pydna.seqrecord.ProteinSeqRecord method) (pydna.seqrecord.SeqRecord method)

J

join() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method)

K

klenow() (pydna.all.Dseq method) (pydna.dseq.Dseq method)

L

lcs() (pydna.seqrecord.SeqRecord method) left_edge (pydna.opencloning_models.SequenceCutSource attribute) left_end_position() (pydna.all.Dseq method) (pydna.dseq.Dseq method) left_location (pydna.opencloning_models.AssemblyFragment attribute) left_ovhg (pydna.all.Dseq property) (pydna.dseq.Dseq property) ligation_assembly() (in module pydna.assembly2) LigationSource (class in pydna.opencloning_models) limit (pydna.all.Anneal attribute) (pydna.amplify.Anneal attribute) limit_iterator() (in module pydna.utils) linearize() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method)

list_features() (pydna.seqrecord.SeqRecord method) list_parts() (in module pydna.fusionpcr) location_boundaries() (in module pydna.utils) locations_overlap() (in module pydna.utils) locstr() (in module pydna.genbankfixer) locus (pydna.seqrecord.SeqRecord property) locus_tag (pydna.opencloning_models.GenomeCoordinatesSource attribute) logo() (in module pydna) looped() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) lower() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method)

M

m() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) M() (pydna.fakeseq.FakeSeq method) m() (pydna.fakeseq.FakeSeq method) main() (in module pydna.threading_timer_decorator_exit) make_automaton() (in module pydna.primer_screen) map_trace_files() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) melt() (pydna.all.Dseq method) (pydna.dseq.Dseq method) melt_ss_dna() (pydna.all.Dseq method) (pydna.dseq.Dseq method) middle (pydna.alphabet.DseqParts attribute) model_config (pydna.opencloning_models.AddgeneIdSource attribute) (pydna.opencloning_models.AnnotationSource attribute) (pydna.opencloning_models.AssemblyFragment attribute) (pydna.opencloning_models.AssemblySource attribute) (pydna.opencloning_models.BenchlingUrlSource attribute) (pydna.opencloning_models.CloningStrategy attribute) (pydna.opencloning_models.ConfiguredBaseModel attribute) (pydna.opencloning_models.CreLoxRecombinationSource attribute) (pydna.opencloning_models.CRISPRSource attribute) (pydna.opencloning_models.DatabaseSource attribute) (pydna.opencloning_models.EuroscarfSource attribute) (pydna.opencloning_models.GatewaySource attribute) (pydna.opencloning_models.GenomeCoordinatesSource attribute) (pydna.opencloning_models.GibsonAssemblySource attribute) (pydna.opencloning_models.HomologousRecombinationSource attribute) (pydna.opencloning_models.IGEMSource attribute) (pydna.opencloning_models.InFusionSource attribute) (pydna.opencloning_models.InVivoAssemblySource attribute) (pydna.opencloning_models.LigationSource attribute) (pydna.opencloning_models.NCBISequenceSource attribute) (pydna.opencloning_models.OligoHybridizationSource attribute) (pydna.opencloning_models.OpenDNACollectionsSource attribute) (pydna.opencloning_models.OverlapExtensionPCRLigationSource attribute) (pydna.opencloning_models.PCRSource attribute) (pydna.opencloning_models.PolymeraseExtensionSource attribute) (pydna.opencloning_models.PrimerModel attribute) (pydna.opencloning_models.RepositoryIdSource attribute) (pydna.opencloning_models.RepositoryIdSourceWithSequenceFileUrl attribute) (pydna.opencloning_models.RestrictionAndLigationSource attribute) (pydna.opencloning_models.ReverseComplementSource attribute) (pydna.opencloning_models.SequenceCutSource attribute) (pydna.opencloning_models.SEVASource attribute) (pydna.opencloning_models.SnapGenePlasmidSource attribute) (pydna.opencloning_models.Source attribute) (pydna.opencloning_models.SourceInput attribute) (pydna.opencloning_models.TextFileSequence attribute) (pydna.opencloning_models.UploadedFileSource attribute) (pydna.opencloning_models.WekWikGeneIdSource attribute)

model_dump() (pydna.opencloning_models.CloningStrategy method) model_dump_json() (pydna.opencloning_models.CloningStrategy method) module pydna pydna.all pydna.alphabet pydna.amplicon pydna.amplify pydna.assembly pydna.assembly2 pydna.codon pydna.common_sub_strings pydna.contig pydna.cre_lox pydna.crispr pydna.design pydna.dseq pydna.dseqrecord pydna.fakeseq pydna.fusionpcr pydna.gateway pydna.gel pydna.genbank pydna.genbankfixer pydna.ladders pydna.oligonucleotide_hybridization pydna.opencloning_models pydna.parsers pydna.primer pydna.primer_screen pydna.readers pydna.seq pydna.seqrecord pydna.sequence_picker pydna.sequence_regex pydna.threading_timer_decorator_exit pydna.tm pydna.types pydna.utils molecular_weight() (pydna.seq.ProteinSeq method) mung() (pydna.all.Dseq method) (pydna.dseq.Dseq method) mw() (pydna.all.Dseq method) (pydna.dseq.Dseq method)

N

n_cutters() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) NCBISequenceSource (class in pydna.opencloning_models) nibble_five_prime_left() (pydna.all.Dseq method) (pydna.dseq.Dseq method) nibble_five_prime_right() (pydna.all.Dseq method) (pydna.dseq.Dseq method) nibble_three_prime_left() (pydna.all.Dseq method) (pydna.dseq.Dseq method) nibble_three_prime_right() (pydna.all.Dseq method) (pydna.dseq.Dseq method)

nibble_to_blunt() (pydna.all.Dseq method) (pydna.dseq.Dseq method) no_cutters() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) node_path2assembly_list() (pydna.assembly2.Assembly method) nucleotide() (pydna.all.Genbank method) (pydna.genbank.Genbank method) number_of_cuts() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method)

O

OligoHybridizationSource (class in pydna.opencloning_models) oligonucleotide_hybridization() (in module pydna.oligonucleotide_hybridization) oligonucleotide_hybridization_overhangs() (in module pydna.oligonucleotide_hybridization) once_cutters() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) open_folder() (in module pydna.utils) OpenDNACollectionsSource (class in pydna.opencloning_models) orfs() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) (pydna.seq.Seq method)

orfs2() (pydna.seq.Seq method) orfs_to_features() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) originstr() (in module pydna.genbankfixer) overhang_crick_3prime (pydna.opencloning_models.OligoHybridizationSource attribute) OverlapExtensionPCRLigationSource (class in pydna.opencloning_models) ovhg (pydna.all.Dseq property) (pydna.crispr.cas9 attribute) (pydna.dseq.Dseq property)

P

pam (pydna.crispr.cas9 attribute) parse() (in module pydna.all) (in module pydna.parsers) parse_primers() (in module pydna.all) (in module pydna.parsers) parse_snapgene() (in module pydna.parsers) parseGBLoc() (in module pydna.genbankfixer) pcr() (in module pydna.all) (in module pydna.amplify) pcr_assembly() (in module pydna.assembly2) pcr_fusion_overlap() (in module pydna.assembly2) PCRAssembly (class in pydna.assembly2) PCRSource (class in pydna.opencloning_models) pfu_sso7d_program() (in module pydna.tm) pI() (pydna.seq.ProteinSeq method) PolymeraseExtensionSource (class in pydna.opencloning_models) Primer (class in pydna.primer) primer_design() (in module pydna.all) (in module pydna.design) primer_pairs() (in module pydna.primer_screen) primer_template_overlap() (in module pydna.assembly2) primer_tuple (class in pydna.primer_screen) PrimerModel (class in pydna.opencloning_models) primers (pydna.opencloning_models.CloningStrategy attribute) primers() (pydna.amplicon.Amplicon method) products (pydna.all.Anneal property) (pydna.amplify.Anneal property) program() (in module pydna.tm) (pydna.amplicon.Amplicon method) ProteinSeq (class in pydna.seq) ProteinSeqRecord (class in pydna.seqrecord) protospacer() (in module pydna.crispr) pydna module pydna.all module pydna.alphabet module pydna.amplicon module pydna.amplify module pydna.assembly module pydna.assembly2 module pydna.codon module pydna.common_sub_strings module pydna.contig module

pydna.cre_lox module pydna.crispr module pydna.design module pydna.dseq module pydna.dseqrecord module pydna.fakeseq module pydna.fusionpcr module pydna.gateway module pydna.gel module pydna.genbank module pydna.genbankfixer module pydna.ladders module pydna.oligonucleotide_hybridization module pydna.opencloning_models module pydna.parsers module pydna.primer module pydna.primer_screen module pydna.readers module pydna.seq module pydna.seqrecord module pydna.sequence_picker module pydna.sequence_regex module pydna.threading_timer_decorator_exit module pydna.tm module pydna.types module pydna.utils module

Q

Q5() (in module pydna.tm)

quick() (pydna.all.Dseq class method) (pydna.dseq.Dseq class method)

R

randomDNA() (in module pydna.utils) randomORF() (in module pydna.utils) randomprot() (in module pydna.utils) randomRNA() (in module pydna.utils) rarecodons() (in module pydna.utils) (pydna.seq.Seq method) (pydna.seqrecord.ProteinSeqRecord method) (pydna.seqrecord.SeqRecord method) rc() (in module pydna.utils) (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.amplicon.Amplicon method) (pydna.contig.Contig method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) (pydna.seq.ProteinSeq method) (pydna.seq.Seq method) (pydna.seqrecord.ProteinSeqRecord method) (pydna.seqrecord.SeqRecord method) reaction_type (pydna.opencloning_models.GatewaySource attribute) read() (in module pydna.all) (in module pydna.readers) read_primer() (in module pydna.all) (in module pydna.readers) reassign_ids() (pydna.opencloning_models.CloningStrategy method) regex_ds_melt_factory() (in module pydna.alphabet) regex_ss_melt_factory() (in module pydna.alphabet) remove_subassemblies() (in module pydna.assembly2) report() (pydna.all.Anneal method) (pydna.amplify.Anneal method) repository_id (pydna.opencloning_models.RepositoryIdSource attribute) RepositoryIdSource (class in pydna.opencloning_models)

RepositoryIdSourceWithSequenceFileUrl (class in pydna.opencloning_models) representation_tuple() (in module pydna.alphabet) restriction_enzymes (pydna.opencloning_models.RestrictionAndLigationSource attribute) restriction_ligation_assembly() (in module pydna.assembly2) restriction_ligation_overlap() (in module pydna.assembly2) RestrictionAndLigationSource (class in pydna.opencloning_models) reverse_complement() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.amplicon.Amplicon method) (pydna.contig.Contig method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) (pydna.primer.Primer method) (pydna.seq.ProteinSeq method) (pydna.seq.Seq method) (pydna.seqrecord.ProteinSeqRecord method) (pydna.seqrecord.SeqRecord method) reverse_complement_assembly() (in module pydna.assembly2) reverse_complement_rna() (pydna.seq.ProteinSeq method) reverse_complemented (pydna.opencloning_models.AssemblyFragment attribute) reverse_primers (pydna.all.Anneal attribute) (pydna.amplify.Anneal attribute) reverse_primers() (in module pydna.primer_screen) ReverseComplementSource (class in pydna.opencloning_models) right_edge (pydna.opencloning_models.SequenceCutSource attribute) right_end_position() (pydna.all.Dseq method) (pydna.dseq.Dseq method) right_location (pydna.opencloning_models.AssemblyFragment attribute) right_ovhg (pydna.all.Dseq property) (pydna.dseq.Dseq property) rp (pydna.primer_screen.amplicon_tuple attribute) (pydna.primer_screen.primer_tuple attribute) rposition (pydna.primer_screen.amplicon_tuple attribute)

S

scaffold (pydna.crispr.cas9 attribute) search() (pydna.crispr.cas9 method) seguid() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) (pydna.seq.ProteinSeq method) (pydna.seq.Seq method) (pydna.seqrecord.SeqRecord method) Seq (class in pydna.seq) seq (pydna.primer_screen.primer_tuple attribute) seq31() (in module pydna.utils) SeqRecord (class in pydna.seqrecord) seqrecord2_uppercase_DNA_string() (in module pydna.assembly2) sequence (pydna.opencloning_models.SourceInput attribute) sequence_file_format (pydna.opencloning_models.UploadedFileSource attribute) sequence_file_url (pydna.opencloning_models.RepositoryIdSourceWithSequenceFileUrl attribute) SequenceCutSource (class in pydna.opencloning_models) SequenceLocationStr (class in pydna.opencloning_models) serialize_coordinates() (pydna.opencloning_models.GenomeCoordinatesSource method) serialize_cut_site() (pydna.opencloning_models.SequenceCutSource method) serialize_input() (pydna.opencloning_models.Source method) serialize_restriction_enzymes() (pydna.opencloning_models.RestrictionAndLigationSource method) set_forward_primer_footprint() (pydna.amplicon.Amplicon method) set_reverse_primer_footprint() (pydna.amplicon.Amplicon method) SEVASource (class in pydna.opencloning_models) shed_ss_dna() (pydna.all.Dseq method) (pydna.dseq.Dseq method) shift_feature() (in module pydna.utils) shift_location() (in module pydna.utils) shifted() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method)

single_crick (pydna.alphabet.DseqParts attribute) single_watson (pydna.alphabet.DseqParts attribute) SingleFragmentAssembly (class in pydna.assembly2) size (pydna.crispr.cas9 attribute) (pydna.primer_screen.amplicon_tuple attribute) (pydna.primer_screen.primer_tuple attribute) smallest_rotation() (in module pydna.utils) SnapGenePlasmidSource (class in pydna.opencloning_models) sorted_features() (pydna.seqrecord.SeqRecord method) Source (class in pydna.opencloning_models) source (pydna.all.Dseqrecord attribute) (pydna.dseqrecord.Dseqrecord attribute) SourceInput (class in pydna.opencloning_models) stamp() (pydna.seqrecord.SeqRecord method) startcodon() (pydna.seq.Seq method) (pydna.seqrecord.ProteinSeqRecord method) (pydna.seqrecord.SeqRecord method) sticky_end_sub_strings() (in module pydna.assembly2) sticky_left3 (pydna.alphabet.DseqParts attribute) sticky_left5 (pydna.alphabet.DseqParts attribute) sticky_right3 (pydna.alphabet.DseqParts attribute) sticky_right5 (pydna.alphabet.DseqParts attribute) stopcodon() (pydna.seq.Seq method) (pydna.seqrecord.ProteinSeqRecord method) (pydna.seqrecord.SeqRecord method) strip_indent() (in module pydna.genbankfixer) strip_multiline() (in module pydna.genbankfixer) subfragment_representation2edge_representation() (in module pydna.assembly2) sum_is_sticky() (in module pydna.utils) synced() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method)

T

T4() (pydna.all.Dseq method) t4() (pydna.all.Dseq method) T4() (pydna.dseq.Dseq method) t4() (pydna.dseq.Dseq method) ta_dbd() (in module pydna.tm) ta_default() (in module pydna.tm) tail (pydna.primer.Primer property) taq_program() (in module pydna.tm) TARGET_MODEL (pydna.opencloning_models.AddgeneIdSource attribute) (pydna.opencloning_models.AnnotationSource attribute) (pydna.opencloning_models.AssemblySource attribute) (pydna.opencloning_models.BenchlingUrlSource attribute) (pydna.opencloning_models.CreLoxRecombinationSource attribute) (pydna.opencloning_models.CRISPRSource attribute) (pydna.opencloning_models.DatabaseSource attribute) (pydna.opencloning_models.EuroscarfSource attribute) (pydna.opencloning_models.GatewaySource attribute) (pydna.opencloning_models.GenomeCoordinatesSource attribute) (pydna.opencloning_models.GibsonAssemblySource attribute) (pydna.opencloning_models.HomologousRecombinationSource attribute) (pydna.opencloning_models.IGEMSource attribute) (pydna.opencloning_models.InFusionSource attribute) (pydna.opencloning_models.InVivoAssemblySource attribute) (pydna.opencloning_models.LigationSource attribute) (pydna.opencloning_models.NCBISequenceSource attribute) (pydna.opencloning_models.OligoHybridizationSource attribute) (pydna.opencloning_models.OpenDNACollectionsSource attribute) (pydna.opencloning_models.OverlapExtensionPCRLigationSource attribute) (pydna.opencloning_models.PCRSource attribute) (pydna.opencloning_models.PolymeraseExtensionSource attribute) (pydna.opencloning_models.RepositoryIdSource attribute) (pydna.opencloning_models.RestrictionAndLigationSource attribute) (pydna.opencloning_models.ReverseComplementSource attribute) (pydna.opencloning_models.SequenceCutSource property) (pydna.opencloning_models.SEVASource attribute) (pydna.opencloning_models.SnapGenePlasmidSource attribute) (pydna.opencloning_models.Source attribute) (pydna.opencloning_models.UploadedFileSource attribute) (pydna.opencloning_models.WekWikGeneIdSource attribute)

template (pydna.all.Anneal attribute) (pydna.amplify.Anneal attribute) terminal_overlap() (in module pydna.assembly2) (in module pydna.common_sub_strings) terminal_transferase() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) TextFileSequence (class in pydna.opencloning_models) three_frame_orfs() (in module pydna.utils) three_prime_end() (pydna.all.Dseq method) (pydna.dseq.Dseq method) tm_dbd() (in module pydna.tm) tm_default() (in module pydna.tm) tm_neb() (in module pydna.tm) tm_product() (in module pydna.tm) tmbresluc() (in module pydna.tm) to_biopython_location() (pydna.opencloning_models.SequenceLocationStr method) to_blunt_string() (pydna.all.Dseq method) (pydna.dseq.Dseq method) to_pydantic_model() (pydna.opencloning_models.AssemblyFragment method) (pydna.opencloning_models.Source method) (pydna.opencloning_models.SourceInput method) to_unserialized_dict() (pydna.opencloning_models.Source method) toGB() (in module pydna.genbankfixer) toInt() (in module pydna.genbankfixer) toJSON() (in module pydna.genbankfixer) tolinear() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) transcribe() (pydna.seq.ProteinSeq method) (pydna.seq.Seq method) translate() (pydna.seq.ProteinSeq method) (pydna.seq.Seq method) (pydna.seqrecord.SeqRecord method) twice_cutters() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method)

U

unique_cutters() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) UploadedFileSource (class in pydna.opencloning_models)

upper() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) user() (pydna.all.Dseq method) (pydna.dseq.Dseq method) user_assembly_design() (in module pydna.design)

W

watson (pydna.all.Dseq property) (pydna.dseq.Dseq property) watson_ovhg (pydna.all.Dseq property) (pydna.dseq.Dseq property)

WekWikGeneIdSource (class in pydna.opencloning_models) wrapstring() (in module pydna.genbankfixer) write() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method)

Z

zip_match_leftwards() (in module pydna.assembly2)

zip_match_rightwards() (in module pydna.assembly2)