Index

A | B | C | D | E | F | G | I | K | L | M | N | O | P | R | S | T | V | W

A

add_feature() (pydna.dsdna.Dseqrecord method)
add_str() (pydna.py_rstr_max.rstr_max.Rstr_max method)
Amplicon (class in pydna.amplify)
analyze_overlaps() (pydna.assembly.Assembly method)
analyze_terminal_overlaps() (pydna.assembly.Assembly method)
Anneal (class in pydna.amplify)
assemble_circular_from_graph() (pydna.assembly.Assembly method)
assemble_fusion_pcr_linear() (pydna.assembly.Assembly method)
assemble_gibson_circular() (pydna.assembly.Assembly method)
assemble_gibson_linear() (pydna.assembly.Assembly method)
assemble_golden_gate() (pydna.assembly.Assembly method)
assemble_hr_circular() (pydna.assembly.Assembly method)
assemble_hr_linear() (pydna.assembly.Assembly method)
assemble_linear_from_graph() (pydna.assembly.Assembly method)
assemble_slic() (pydna.assembly.Assembly method)
Assembly (class in pydna.assembly)
assembly_primers() (in module pydna.primer_design)

B

basictm() (in module pydna.amplify)

C

ChenFoxLyndon() (in module pydna.utils)
ChenFoxLyndonBreakpoints() (in module pydna.utils)
circular (pydna.dsdna.Dseq attribute)
(pydna.dsdna.Dseqrecord attribute)
cloning_primers() (in module pydna.primer_design)
common_sub_strings() (in module pydna.findsubstrings_suffix_arrays_python)
Contig (class in pydna.assembly)
copy_features() (in module pydna.utils)
create_graph() (pydna.assembly.Assembly method)
cseguid() (in module pydna.utils)
(pydna.dsdna.Dseqrecord method)
cut() (pydna.dsdna.Dseq method)
(pydna.dsdna.Dseqrecord method)

D

detailed_fig() (pydna.assembly.Contig method)
detailed_figure() (pydna.assembly.Contig method)
direct_kark_sort() (in module pydna.py_rstr_max.tools_karkkainen_sanders)
Dseq (class in pydna.dsdna)
Dseqrecord (class in pydna.dsdna)
dsrecs (pydna.assembly.Assembly attribute)

E

Editor (class in pydna.editor)
eq() (in module pydna.utils)
extract_feature() (pydna.dsdna.Dseqrecord method)

F

fig() (pydna.dsdna.Dseq method)
figure() (pydna.amplify.Amplicon method)
fill_in() (pydna.dsdna.Dseq method)
find() (pydna.dsdna.Dseq method)
five_prime_end() (pydna.dsdna.Dseq method)
flankdn() (pydna.amplify.Amplicon method)
flankup() (pydna.amplify.Amplicon method)
format() (pydna.dsdna.Dseqrecord method)
Fragment (class in pydna.assembly)

G

Genbank (class in pydna.download)
go() (pydna.py_rstr_max.rstr_max.Rstr_max method)

I

isorf() (pydna.dsdna.Dseqrecord method)

K

kark_sort() (in module pydna.py_rstr_max.tools_karkkainen_sanders)

L

LCP() (in module pydna.py_rstr_max.tools_karkkainen_sanders)
limit (pydna.assembly.Assembly attribute)
linear (pydna.dsdna.Dseq attribute)
(pydna.dsdna.Dseqrecord attribute)
linearize() (pydna.dsdna.Dseqrecord method)
list_features() (pydna.dsdna.Dseqrecord method)
looped() (pydna.dsdna.Dseq method)
(pydna.dsdna.Dseqrecord method)

M

max_nodes (pydna.assembly.Assembly attribute)
mung() (pydna.dsdna.Dseq method)

N

nucleotide() (pydna.download.Genbank method)

O

open() (pydna.editor.Editor method)
ovhg (pydna.dsdna.Dseq attribute)

P

pairwise() (in module pydna.utils)
parse() (in module pydna.dsdna)
parse_new() (in module pydna.dsdna)
pcr() (in module pydna.amplify)
Primer (class in pydna.amplify)
primer_pair() (in module pydna.primer_design)
products (pydna.amplify.Anneal attribute)
program() (pydna.amplify.Amplicon method)
pydna (module)
pydna.amplify (module)
pydna.assembly (module)
pydna.download (module)
pydna.dsdna (module)
pydna.editor (module)
pydna.findsubstrings_suffix_arrays_python (module)
pydna.primer_design (module)
pydna.py_rstr_max (module)
pydna.py_rstr_max.rstr_max (module)
pydna.py_rstr_max.tools_karkkainen_sanders (module)
pydna.utils (module)

R

radixpass() (in module pydna.py_rstr_max.tools_karkkainen_sanders)
rc() (in module pydna.dsdna)
(pydna.dsdna.Dseq method)
(pydna.dsdna.Dseqrecord method)
read() (in module pydna.dsdna)
removeMany() (pydna.py_rstr_max.rstr_max.Rstr_max method)
report() (pydna.amplify.Anneal method)
reverse_complement() (pydna.dsdna.Dseq method)
(pydna.dsdna.Dseqrecord method)
Rstr_max (class in pydna.py_rstr_max.rstr_max)

S

seguid() (pydna.dsdna.Dseqrecord method)
shift_origin() (in module pydna.utils)
shifted() (pydna.dsdna.Dseqrecord method)
simple_kark_sort() (in module pydna.py_rstr_max.tools_karkkainen_sanders)
small_fig() (pydna.assembly.Contig method)
small_figure() (pydna.assembly.Contig method)
SmallestRotation() (in module pydna.utils)
stamp() (pydna.dsdna.Dseqrecord method)
step1_sort_suffix() (pydna.py_rstr_max.rstr_max.Rstr_max method)
step2_lcp() (pydna.py_rstr_max.rstr_max.Rstr_max method)
step3_rstr() (pydna.py_rstr_max.rstr_max.Rstr_max method)
synced() (pydna.dsdna.Dseqrecord method)

T

t4() (pydna.dsdna.Dseq method)
T4() (pydna.dsdna.Dseq method)
terminal_overlap() (in module pydna.findsubstrings_suffix_arrays_python)
test() (pydna.download.Genbank method)
three_prime_end() (pydna.dsdna.Dseq method)
tmbreslauer86() (in module pydna.amplify)
tmbresluc() (in module pydna.amplify)
tmstaluc98() (in module pydna.amplify)
tolinear() (pydna.dsdna.Dseq method)
(pydna.dsdna.Dseqrecord method)

V

verify_stamp() (pydna.dsdna.Dseqrecord method)

W

write() (pydna.dsdna.Dseqrecord method)