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) Amplicon (class in pydna.amplicon) Anneal (class in pydna.all) (class in pydna.amplify) annotate_gateway_sites() (in module pydna.gateway) annotate_loxP_sites() (in module pydna.cre_lox) annotate_primer_binding_sites() (in module pydna.assembly2) annotations (pydna.dseqrecord.Dseqrecord attribute) 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) 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_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)

BASE_MODEL (pydna.opencloning_models.SequenceCutSource attribute) biopython_code() (pydna.genbankrecord.GenbankRecord method) 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) cas9 (class in pydna.crispr) cas9() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord 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) CloningStrategy (class in pydna.opencloning_models) 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) 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) 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) 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) 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)

download_text() (in module pydna.all) (in module pydna.download) Dseq (class in pydna.all) (class in pydna.dseq) 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) ENZYME_MODEL (pydna.opencloning_models.SequenceCutSource attribute) eq() (in module pydna.all) (in module pydna.utils) 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)

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) fill_dseq() (in module pydna.assembly2) fill_in() (pydna.all.Dseq method) (pydna.dseq.Dseq method) fill_left() (in module pydna.assembly2) fill_right() (in module pydna.assembly2) filter_linear_subassemblies() (in module pydna.assembly2) find() (pydna.all.Dseq method) (pydna.all.Dseqrecord 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) 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) 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) (pydna.genbankfile.GenbankFile class method) (pydna.genbankrecord.GenbankRecord class method) from_start_and_end() (pydna.opencloning_models.SequenceLocationStr class method) from_string() (pydna.all.Dseq class method) (pydna.all.Dseqrecord class method) (pydna.contig.Contig class method) (pydna.dseq.Dseq class method) (pydna.dseqrecord.Dseqrecord class method) (pydna.genbankrecord.GenbankRecord 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) GenbankFile (class in pydna.genbankfile) GenbankRecord (class in pydna.genbankrecord) 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_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_possible_assembly_number() (pydna.assembly2.Assembly method) get_regex_dict() (in module pydna.cre_lox) 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) in_fusion_assembly() (in module pydna.assembly2) in_vivo_assembly() (in module pydna.assembly2) InFusionSource (class in pydna.opencloning_models) input (pydna.opencloning_models.Source attribute) input_models() (pydna.opencloning_models.Source method)

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)

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) ligate() (in module pydna.ligate) 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) logo() (in module pydna) looped() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) lower() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq 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) map_trace_files() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) model_config (pydna.opencloning_models.AssemblyFragment attribute) (pydna.opencloning_models.AssemblySource attribute) (pydna.opencloning_models.CloningStrategy attribute) (pydna.opencloning_models.ConfiguredBaseModel attribute) (pydna.opencloning_models.CreLoxRecombinationSource attribute) (pydna.opencloning_models.CRISPRSource attribute) (pydna.opencloning_models.GatewaySource attribute) (pydna.opencloning_models.GibsonAssemblySource attribute) (pydna.opencloning_models.HomologousRecombinationSource attribute) (pydna.opencloning_models.InFusionSource attribute) (pydna.opencloning_models.InVivoAssemblySource attribute) (pydna.opencloning_models.LigationSource attribute) (pydna.opencloning_models.OverlapExtensionPCRLigationSource attribute) (pydna.opencloning_models.PCRSource attribute) (pydna.opencloning_models.PrimerModel attribute) (pydna.opencloning_models.RestrictionAndLigationSource attribute) (pydna.opencloning_models.SequenceCutSource attribute) (pydna.opencloning_models.Source attribute) (pydna.opencloning_models.SourceInput attribute) (pydna.opencloning_models.TextFileSequence attribute) model_dump() (pydna.opencloning_models.CloningStrategy method) model_dump_json() (pydna.opencloning_models.CloningStrategy method) module pydna pydna.all pydna.amplicon pydna.amplify pydna.assembly pydna.assembly2 pydna.codon pydna.common_sub_strings pydna.conftest pydna.contig pydna.cre_lox pydna.crispr pydna.design pydna.download pydna.dseq pydna.dseqrecord pydna.fakeseq pydna.fusionpcr pydna.gateway pydna.gel pydna.genbank pydna.genbankfile pydna.genbankfixer pydna.genbankrecord pydna.goldengate pydna.ladders pydna.ligate pydna.opencloning_models pydna.parsers pydna.primer pydna.readers pydna.seq pydna.seqrecord pydna.sequence_picker pydna.sequence_regex pydna.threading_timer_decorator_exit pydna.tm pydna.types pydna.user_cloning 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) 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

once_cutters() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) open_folder() (in module pydna.utils) 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) OverlapExtensionPCRLigationSource (class in pydna.opencloning_models) ovhg (pydna.crispr.cas9 attribute)

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) PCRAssembly (class in pydna.assembly2) PCRSource (class in pydna.opencloning_models) pfu_sso7d_program() (in module pydna.tm) pI() (pydna.seq.ProteinSeq method) Primer (class in pydna.primer) primer_design() (in module pydna.all) (in module pydna.design) primer_template_overlap() (in module pydna.assembly2) 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.amplicon module pydna.amplify module pydna.assembly module pydna.assembly2 module pydna.codon module pydna.common_sub_strings module pydna.conftest module pydna.contig module pydna.cre_lox module pydna.crispr module pydna.design module

pydna.download module pydna.dseq module pydna.dseqrecord module pydna.fakeseq module pydna.fusionpcr module pydna.gateway module pydna.gel module pydna.genbank module pydna.genbankfile module pydna.genbankfixer module pydna.genbankrecord module pydna.goldengate module pydna.ladders module pydna.ligate module pydna.opencloning_models module pydna.parsers module pydna.primer 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.user_cloning module pydna.utils module pydna_code() (pydna.genbankrecord.GenbankRecord method)

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.genbankfile.GenbankFile method) (pydna.genbankrecord.GenbankRecord 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) remove_subassemblies() (in module pydna.assembly2)

report() (pydna.all.Anneal method) (pydna.amplify.Anneal method) 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.genbankfile.GenbankFile method) (pydna.genbankrecord.GenbankRecord 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) 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)

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) seq31() (in module pydna.utils) SeqRecord (class in pydna.seqrecord) seqrecord2_uppercase_DNA_string() (in module pydna.assembly2) sequence (pydna.opencloning_models.SourceInput attribute) SequenceCutSource (class in pydna.opencloning_models) SequenceLocationStr (class in pydna.opencloning_models) set_forward_primer_footprint() (pydna.amplicon.Amplicon method) set_reverse_primer_footprint() (pydna.amplicon.Amplicon 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)

SingleFragmentAssembly (class in pydna.assembly2) size (pydna.crispr.cas9 attribute) smallest_rotation() (in module pydna.utils) 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) 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.AssemblySource attribute) (pydna.opencloning_models.CreLoxRecombinationSource attribute) (pydna.opencloning_models.CRISPRSource attribute) (pydna.opencloning_models.GatewaySource attribute) (pydna.opencloning_models.GibsonAssemblySource attribute) (pydna.opencloning_models.HomologousRecombinationSource attribute) (pydna.opencloning_models.InFusionSource attribute) (pydna.opencloning_models.InVivoAssemblySource attribute) (pydna.opencloning_models.LigationSource attribute) (pydna.opencloning_models.OverlapExtensionPCRLigationSource attribute) (pydna.opencloning_models.PCRSource attribute) (pydna.opencloning_models.RestrictionAndLigationSource attribute) (pydna.opencloning_models.Source attribute) template (pydna.all.Anneal attribute) (pydna.amplify.Anneal attribute) terminal_overlap() (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_pydantic_model() (pydna.opencloning_models.AssemblyFragment method) (pydna.opencloning_models.AssemblySource method) (pydna.opencloning_models.SequenceCutSource method) (pydna.opencloning_models.Source method) (pydna.opencloning_models.SourceInput method) toGB() (in module pydna.genbankfixer) toInt() (in module pydna.genbankfixer) toJSON() (in module pydna.genbankfixer) tolinear() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) transcribe() (pydna.all.Dseq method) (pydna.dseq.Dseq method) (pydna.seq.ProteinSeq method) translate() (pydna.all.Dseq method) (pydna.dseq.Dseq method) (pydna.seq.ProteinSeq method) (pydna.seq.Seq method) (pydna.seqrecord.SeqRecord method) trunc (pydna.all.Dseq attribute) (pydna.dseq.Dseq attribute) 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)

upper() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method)

W

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

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)