Index

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

A

add_str() (pydna.py_rstr_max.rstr_max.Rstr_max method)
AgaroseGel() (in module pydna.gel)
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)
BORDER (pydna.gel.Gel attribute)

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)
expose() (pydna.gel.Gel 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

gamma() (in module pydna.gel)
Gel (class in pydna.gel)
Genbank (class in pydna.download)
go() (pydna.py_rstr_max.rstr_max.Rstr_max method)

K

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

L

LANE_HEIGHT (pydna.gel.Gel attribute)
LANE_MARGIN (pydna.gel.Gel attribute)
LANE_WIDTH (pydna.gel.Gel attribute)
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)
loadSample() (pydna.gel.Gel 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)
pcr() (in module pydna.amplify)
Primer (class in pydna.amplify)
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.gel (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)
run() (pydna.gel.Gel method)

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)
sync() (in module pydna.utils)
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)
testColour() (in module pydna.gel)
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)