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 0xb786a76c>,
 2: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb786aa2c>,
 3: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb786acec>,
 4: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb786afac>,
 5: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb786c28c>,
 6: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb786c54c>,
 9: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb786c80c>,
 10: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb786cacc>,
...                                                                    

ambiguous_dna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.AmbiguousCodonTable\
 instance at 0xb786036c>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.AmbiguousCodonTable in\
stance at 0xb785af0c>,
 'Bacterial': <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb\
786a1ec>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.AmbiguousCodonTable \
instance at 0xb785ca6c>,
...                                                                    

ambiguous_rna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb76cc64c>,
 2: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb76cc90c>,
 3: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb76ccbcc>,
 4: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb76cce8c>,
 5: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb76da16c>,
 6: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb76da42c>,
 9: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb76da6ec>,
 10: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb76da9ac>,
...                                                                    

ambiguous_rna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.AmbiguousCodonTable\
 instance at 0xb76c524c>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.AmbiguousCodonTable in\
stance at 0xb76c1b6c>,
 'Bacterial': <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb\
76cc0cc>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.AmbiguousCodonTable \
instance at 0xb76cb94c>,
...                                                                    

standard_dna_table

Type:
NCBICodonTableDNA
Value:
<Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb756decc>         

standard_rna_table

Type:
NCBICodonTableRNA
Value:
<Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb756de2c>         

unambiguous_dna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb756decc>,
 2: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb75a7ecc>,
 3: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb786946c>,
 4: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb786996c>,
 5: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb7869f4c>,
 6: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb76b250c>,
 9: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb76b2a0c>,
 10: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb76b2f0c>,
...                                                                    

unambiguous_dna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTableDNA i\
nstance at 0xb76bd9ec>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTableDNA inst\
ance at 0xb76bdf0c>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb76\
bd42c>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTableDNA in\
stance at 0xb785a94c>,
...                                                                    

unambiguous_rna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb756de2c>,
 2: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb75a7eec>,
 3: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb786948c>,
 4: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb786998c>,
 5: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb7869f6c>,
 6: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb76b252c>,
 9: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb76b2a2c>,
 10: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb76b2f2c>,
...                                                                    

unambiguous_rna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTableRNA i\
nstance at 0xb76bda0c>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTableRNA inst\
ance at 0xb76bdf2c>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb76\
bd44c>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTableRNA in\
stance at 0xb785ae8c>,
...                                                                    

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