Package Bio :: Package Data :: Module CodonTable
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Module Bio.Data.CodonTable

Classes
AmbiguousCodonTable  
AmbiguousForwardTable  
CodonTable  
NCBICodonTable  
NCBICodonTableDNA  
NCBICodonTableRNA  

Exceptions
TranslationError  

Function Summary
  list_ambiguous_codons(codons)
  list_possible_proteins(codon, forward_table, ambiguous_nucleotide_values)
  make_back_table(table, default_stop_codon)
  register_ncbi_table(name, alt_name, id, table, start_codons, stop_codons)

Variable Summary
dict ambiguous_dna_by_id = {1: <Bio.Data.CodonTable.Ambiguous...
dict ambiguous_dna_by_name = {'Ascidian Mitochondrial': <Bio....
dict ambiguous_rna_by_id = {1: <Bio.Data.CodonTable.Ambiguous...
dict ambiguous_rna_by_name = {'Ascidian Mitochondrial': <Bio....
dict generic_by_id = {1: <Bio.Data.CodonTable.NCBICodonTable ...
dict generic_by_name = {'Ascidian Mitochondrial': <Bio.Data.C...
NCBICodonTableDNA standard_dna_table = <Bio.Data.CodonTable.NCBICodonTable...
NCBICodonTableRNA standard_rna_table = <Bio.Data.CodonTable.NCBICodonTable...
dict unambiguous_dna_by_id = {1: <Bio.Data.CodonTable.NCBICod...
dict unambiguous_dna_by_name = {'Ascidian Mitochondrial': <Bi...
dict unambiguous_rna_by_id = {1: <Bio.Data.CodonTable.NCBICod...
dict unambiguous_rna_by_name = {'Ascidian Mitochondrial': <Bi...

Variable Details

ambiguous_dna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705ad238>,
 2: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705ad5a8>,
 3: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705ad918>,
 4: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705adc88>,
 5: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705ae030>,
 6: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705ae3a0>,
 9: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705ae710>,
 10: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705aea80>,
...                                                                    

ambiguous_dna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.AmbiguousCodonTable\
 instance at 0x705a94e0>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.AmbiguousCodonTable in\
stance at 0x70595418>,
 'Bacterial': <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x7\
05abb20>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.AmbiguousCodonTable \
instance at 0x705a6580>,
...                                                                    

ambiguous_rna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705bcd78>,
 2: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705c2120>,
 3: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705c2490>,
 4: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705c2800>,
 5: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705c2b70>,
 6: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705c2ee0>,
 9: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705c5288>,
 10: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x705c55f8>,
...                                                                    

ambiguous_rna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.AmbiguousCodonTable\
 instance at 0x705b7058>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.AmbiguousCodonTable in\
stance at 0x705aff58>,
 'Bacterial': <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x7\
05bc698>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.AmbiguousCodonTable \
instance at 0x705b50f8>,
...                                                                    

generic_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTable instance at 0x705b35d0>,
 2: <Bio.Data.CodonTable.NCBICodonTable instance at 0x706f6670>,
 3: <Bio.Data.CodonTable.NCBICodonTable instance at 0x706f66e8>,
 4: <Bio.Data.CodonTable.NCBICodonTable instance at 0x706f67b0>,
 5: <Bio.Data.CodonTable.NCBICodonTable instance at 0x706f6828>,
 6: <Bio.Data.CodonTable.NCBICodonTable instance at 0x706f68f0>,
 9: <Bio.Data.CodonTable.NCBICodonTable instance at 0x706f6968>,
 10: <Bio.Data.CodonTable.NCBICodonTable instance at 0x706f6a08>,
...                                                                    

generic_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTable inst\
ance at 0x706f6dc8>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTable instanc\
e at 0x706f6fa8>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTable instance at 0x706f6b\
e8>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTable insta\
nce at 0x705953a0>,
...                                                                    

standard_dna_table

Type:
NCBICodonTableDNA
Value:
<Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x705b3580>         

standard_rna_table

Type:
NCBICodonTableRNA
Value:
<Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x705b36c0>         

unambiguous_dna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x705b3580>,
 2: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x705b36e8>,
 3: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x706f66c0>,
 4: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x706f6788>,
 5: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x706f6800>,
 6: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x706f68c8>,
 9: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x706f6940>,
 10: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x706f69e0>,
...                                                                    

unambiguous_dna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTableDNA i\
nstance at 0x706f6cd8>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTableDNA inst\
ance at 0x706f6eb8>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x706\
f6af8>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTableDNA in\
stance at 0x705952b0>,
...                                                                    

unambiguous_rna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x705b36c0>,
 2: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x706f6698>,
 3: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x706f6710>,
 4: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x706f67d8>,
 5: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x706f6850>,
 6: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x706f6918>,
 9: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x706f6990>,
 10: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x706f6a30>,
...                                                                    

unambiguous_rna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTableRNA i\
nstance at 0x706f6e18>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTableRNA inst\
ance at 0x70595030>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x706\
f6c38>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTableRNA in\
stance at 0x705953f0>,
...                                                                    

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