Index

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

A

add() (pydna.orderedset.OrderedSet method)
add_feature() (pydna.dsdna.Dseqrecord method)
add_str() (pydna.py_rstr_max.rstr_max.Rstr_max method)
Amplicon (class in pydna.amplify)
Anneal (class in pydna.amplify)
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)
cseguid() (in module pydna.utils)
(pydna.dsdna.Dseqrecord method)
cut() (pydna.dsdna.Dseq method)
(pydna.dsdna.Dseqrecord method)

D

dbd_program() (pydna.amplify.Amplicon method)
detailed_fig() (pydna.assembly.Contig method)
detailed_figure() (pydna.assembly.Contig method)
direct_kark_sort() (in module pydna.py_rstr_max.tools_karkkainen_sanders)
discard() (pydna.orderedset.OrderedSet method)
download() (pydna.download.web method)
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)
(pydna.assembly.Contig method)
fill_in() (pydna.dsdna.Dseq method)
find() (pydna.dsdna.Dseq method)
find_aa() (pydna.dsdna.Dseqrecord method)
find_aminoacids() (pydna.dsdna.Dseqrecord method)
find_module() (pydna.ipynb_importer.NotebookFinder method)
find_notebook() (in module pydna.ipynb_importer)
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

gc() (pydna.dsdna.Dseqrecord method)
Genbank (class in pydna.download)
GenbankRecord (class in pydna.download)
go() (pydna.py_rstr_max.rstr_max.Rstr_max method)

I

integration_primers() (in module pydna.primer_design)
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)
load_module() (pydna.ipynb_importer.NotebookLoader method)
looped() (pydna.dsdna.Dseq method)
(pydna.dsdna.Dseqrecord method)

M

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

N

nopcr() (in module pydna.amplify)
NotebookFinder (class in pydna.ipynb_importer)
NotebookLoader (class in pydna.ipynb_importer)
nucleotide() (pydna.download.Genbank method)
number_of_cuts() (pydna.dsdna.Dseqrecord method)

O

olaps() (pydna.dsdna.Dseqrecord method)
only_terminal_overlaps (pydna.assembly.Assembly attribute)
open() (pydna.editor.Editor method)
OrderedSet (class in pydna.orderedset)
ovhg (pydna.dsdna.Dseq attribute)

P

pairwise() (in module pydna.utils)
parse() (in module pydna.dsdna)
parse2() (in module pydna.dsdna)
pcr() (in module pydna.amplify)
pop() (pydna.orderedset.OrderedSet method)
pretty_str (class in pydna.pretty)
pretty_string (class in pydna.pretty)
pretty_unicode (class in pydna.pretty)
Primer (class in pydna.amplify)
(class in pydna.primer_design)
print_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.ipynb_importer (module)
pydna.orderedset (module)
pydna.pretty (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.thermodynamic_data (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)
spread_ape_colors() (pydna.dsdna.Dseqrecord method)
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)
taq_program() (pydna.amplify.Amplicon 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)

U

url() (pydna.download.GenbankRecord method)

V

verify_stamp() (pydna.dsdna.Dseqrecord method)

W

web (class in pydna.download)
write() (pydna.dsdna.Dseqrecord method)