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....
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 0x40a00a2c>,
 2: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a00cec>,
 3: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a00fac>,
 4: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a0228c>,
 5: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a0254c>,
 6: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a0280c>,
 9: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a02acc>,
 10: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a02d8c>,
...                                                                    

ambiguous_dna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.AmbiguousCodonTable\
 instance at 0x408bc62c>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.AmbiguousCodonTable in\
stance at 0x408b41ec>,
 'Bacterial': <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x4\
0a004ac>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.AmbiguousCodonTable \
instance at 0x408b4d2c>,
...                                                                    

ambiguous_rna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a2e90c>,
 2: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a2ebcc>,
 3: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a2ee8c>,
 4: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a3016c>,
 5: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a3042c>,
 6: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a306ec>,
 9: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a309ac>,
 10: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x40a30c6c>,
...                                                                    

ambiguous_rna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.AmbiguousCodonTable\
 instance at 0x40a2050c>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.AmbiguousCodonTable in\
stance at 0x40a0ae2c>,
 'Bacterial': <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0x4\
0a2e38c>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.AmbiguousCodonTable \
instance at 0x40a1cc0c>,
...                                                                    

standard_dna_table

Type:
NCBICodonTableDNA
Value:
<Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x40b6126c>         

standard_rna_table

Type:
NCBICodonTableRNA
Value:
<Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x40b6116c>         

unambiguous_dna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x40b6126c>,
 2: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x40a031ac>,
 3: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x40a0372c>,
 4: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x40a03c2c>,
 5: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x40a1522c>,
 6: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x40a157cc>,
 9: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x40a15ccc>,
 10: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x40a0b1ec>,
...                                                                    

unambiguous_dna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTableDNA i\
nstance at 0x40a0bcac>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTableDNA inst\
ance at 0x408b21ec>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0x40a\
0b6ec>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTableDNA in\
stance at 0x408b2c0c>,
...                                                                    

unambiguous_rna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x40b6116c>,
 2: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x40a031cc>,
 3: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x40a0374c>,
 4: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x40a03c4c>,
 5: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x40a1524c>,
 6: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x40a157ec>,
 9: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x40a15cec>,
 10: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x40a0b20c>,
...                                                                    

unambiguous_rna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTableRNA i\
nstance at 0x40a0bccc>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTableRNA inst\
ance at 0x408b220c>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0x40a\
0b70c>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTableRNA in\
stance at 0x408b416c>,
...                                                                    

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