Index

A

a() (in module pydna.threading_timer_decorator_exit) accessed (pydna.all.PrimerList property) (pydna.myprimers.PrimerList property) accession (pydna.seqrecord.SeqRecord property) add_colors_to_features_for_ape() (pydna.seqrecord.SeqRecord method) add_feature() (pydna.all.Dseqrecord method) (pydna.dseqrecord.Dseqrecord method) (pydna.seqrecord.SeqRecord method) Amplicon (class in pydna.amplicon) Anneal (class in pydna.all) (class in pydna.amplify) ape() (in module pydna.all) (in module pydna.editor)

apply_cut() (pydna.all.Dseq method) (pydna.all.Dseqrecord method) (pydna.dseq.Dseq method) (pydna.dseqrecord.Dseqrecord method) assemble_circular() (pydna.all.Assembly method) (pydna.assembly.Assembly method) assemble_linear() (pydna.all.Assembly method) (pydna.assembly.Assembly method) Assembly (class in pydna.all) (class in pydna.assembly) assembly_fragments() (in module pydna.all) (in module pydna.design) assign_numbers() (pydna.all.PrimerList method) (pydna.myprimers.PrimerList method)

B

b() (in module pydna.threading_timer_decorator_exit)

back_transcribe() (pydna.seq.ProteinSeq method) biopython_code() (pydna.genbankrecord.GenbankRecord method)

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) check_primer_numbers() (in module pydna.myprimers) circular (pydna.all.Dseqrecord property) (pydna.dseqrecord.Dseqrecord property) circular_assembly_fragments() (in module pydna.all) (in module pydna.design) code() (pydna.all.PrimerList method) (pydna.myprimers.PrimerList method) comment() (pydna.seqrecord.SeqRecord method) common_sub_strings() (in module pydna.common_sub_strings) complement() (in module pydna.utils) (pydna.seq.ProteinSeq method)

complement_rna() (pydna.seq.ProteinSeq method) concat_dict() (in module pydna.genbankfixer) 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) 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) definition (pydna.seqrecord.SeqRecord property) detailed_figure() (pydna.contig.Contig method)

download_text() (in module pydna.all) Dseq (class in pydna.all) (class in pydna.dseq) Dseqrecord (class in pydna.all) (class in pydna.dseqrecord) dump() (pydna.seqrecord.SeqRecord method)

E

Editor (class in pydna.editor) embl_gb_fasta() (in module pydna.parsers) 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)

F

FakeSeq (class in pydna.fakeseq) figure() (pydna.all.Dseqrecord method) (pydna.amplicon.Amplicon method) (pydna.contig.Contig method) (pydna.dseqrecord.Dseqrecord method) fill_in() (pydna.all.Dseq method) (pydna.dseq.Dseq method) 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_duplicate_primers() (in module pydna.myprimers) 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)

forward_primers (pydna.all.Anneal attribute) (pydna.amplify.Anneal attribute) from_Bio_SeqRecord() (pydna.seqrecord.SeqRecord class method) from_full_sequence_and_overhangs() (pydna.all.Dseq class method) (pydna.dseq.Dseq 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_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) fst3 (pydna.crispr.cas9 attribute) fst5 (pydna.crispr.cas9 attribute) fuse_by_pcr() (in module pydna.fusionpcr)

G

Gateway (class in pydna.gateway) 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_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)

I

identifier_from_string() (in module pydna.utils) instability_index() (pydna.seq.ProteinSeq method) interpolator() (in module pydna.gel)

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_end_position() (pydna.all.Dseq method) (pydna.dseq.Dseq method) ligate() (in module pydna.ligate) limit (pydna.all.Anneal attribute) (pydna.amplify.Anneal attribute) 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) lol() (pydna._pretty.PrettyTable method) 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) memorize() (in module pydna.utils) module pydna pydna._pretty pydna._thermodynamic_data pydna.all pydna.amplicon pydna.amplify pydna.assembly pydna.codon pydna.common_sub_strings pydna.conftest pydna.contig pydna.crispr pydna.design pydna.download pydna.dseq pydna.dseqrecord pydna.editor pydna.fakeseq pydna.fusionpcr pydna.gateway pydna.gel pydna.genbank pydna.genbankfile pydna.genbankfixer pydna.genbankrecord pydna.goldengate pydna.ladders pydna.ligate pydna.myenzymes pydna.myprimers pydna.parsers pydna.primer pydna.readers pydna.seq pydna.seqrecord pydna.sequence_picker pydna.threading_timer_decorator_exit pydna.tm 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)

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() (pydna.editor.Editor method) open_cache_folder() (in module pydna) open_config_folder() (in module pydna) open_current_folder() (in module pydna) open_folder() (in module pydna.utils) (pydna.all.PrimerList method) (pydna.myprimers.PrimerList method)

open_log_folder() (in module pydna) 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) 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) parseGBLoc() (in module pydna.genbankfixer) pcr() (in module pydna.all) (in module pydna.amplify) pfu_sso7d_program() (in module pydna.tm) pI() (pydna.seq.ProteinSeq method) pretty_str (class in pydna._pretty) PrettyTable (class in pydna._pretty) Primer (class in pydna.primer) primer_design() (in module pydna.all) (in module pydna.design) PrimerList (class in pydna.all) (class in pydna.myprimers) 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._pretty module pydna._thermodynamic_data module pydna.all module pydna.amplicon module pydna.amplify module pydna.assembly module pydna.codon module pydna.common_sub_strings module pydna.conftest module pydna.contig module pydna.crispr module pydna.design module pydna.download module pydna.dseq module

pydna.dseqrecord module pydna.editor 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.myenzymes module pydna.myprimers module pydna.parsers module pydna.primer module pydna.readers module pydna.seq module pydna.seqrecord module pydna.sequence_picker module pydna.threading_timer_decorator_exit module pydna.tm module pydna.user_cloning module pydna.utils module pydna_code() (pydna.genbankrecord.GenbankRecord method) pydna_code_from_list() (pydna.all.PrimerList method) (pydna.myprimers.PrimerList 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) read() (in module pydna.all) (in module pydna.readers)

read_primer() (in module pydna.all) (in module pydna.readers) report() (pydna.all.Anneal method) (pydna.amplify.Anneal method) 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_rna() (pydna.seq.ProteinSeq method) reverse_primers (pydna.all.Anneal attribute) (pydna.amplify.Anneal attribute) right_end_position() (pydna.all.Dseq method) (pydna.dseq.Dseq method)

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) 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)

size (pydna.crispr.cas9 attribute) smallest_rotation() (in module pydna.utils) sorted_features() (pydna.seqrecord.SeqRecord method) stamp() (pydna.seqrecord.SeqRecord method) startcodon() (pydna.seq.Seq method) (pydna.seqrecord.ProteinSeqRecord method) (pydna.seqrecord.SeqRecord method) 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) 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) 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) 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) 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

undefined_sequence() (in module pydna.myprimers) 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)