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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 0xb7909c4c>,
 2: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7909f0c>,
 3: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b261ec>,
 4: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b264ac>,
 5: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b2676c>,
 6: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b26a2c>,
 9: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b26cec>,
 10: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b26fac>,
...

ambiguous_dna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.AmbiguousCodonTable\
 instance at 0xb7b1584c>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.AmbiguousCodonTable in\
stance at 0xb7b9040c>,
 'Bacterial': <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb\
79096cc>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.AmbiguousCodonTable \
instance at 0xb7b90f4c>,
...

ambiguous_rna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b36b2c>,
 2: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b36dec>,
 3: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b380cc>,
 4: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b3838c>,
 5: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b3864c>,
 6: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b3890c>,
 9: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b38bcc>,
 10: <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb7b38e8c>,
...

ambiguous_rna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.AmbiguousCodonTable\
 instance at 0xb7b3272c>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.AmbiguousCodonTable in\
stance at 0xb7b2a06c>,
 'Bacterial': <Bio.Data.CodonTable.AmbiguousCodonTable instance at 0xb\
7b365ac>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.AmbiguousCodonTable \
instance at 0xb7b2ae2c>,
...

generic_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTable instance at 0xb7b3534c>,
 2: <Bio.Data.CodonTable.NCBICodonTable instance at 0xb7890d2c>,
 3: <Bio.Data.CodonTable.NCBICodonTable instance at 0xb7b8b2ec>,
 4: <Bio.Data.CodonTable.NCBICodonTable instance at 0xb7b8b80c>,
 5: <Bio.Data.CodonTable.NCBICodonTable instance at 0xb7b8be0c>,
 6: <Bio.Data.CodonTable.NCBICodonTable instance at 0xb7b873ec>,
 9: <Bio.Data.CodonTable.NCBICodonTable instance at 0xb7b8790c>,
 10: <Bio.Data.CodonTable.NCBICodonTable instance at 0xb7b87e2c>,
...

generic_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTable inst\
ance at 0xb7b8a06c>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTable instanc\
e at 0xb7b8a6ac>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTable instance at 0xb7b889\
ec>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTable insta\
nce at 0xb7b9034c>,
...

standard_dna_table

Type:
NCBICodonTableDNA
Value:
<Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb7b3532c>

standard_rna_table

Type:
NCBICodonTableRNA
Value:
<Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb7890cec>

unambiguous_dna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb7b3532c>,
 2: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb7890d0c>,
 3: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb7b8b2cc>,
 4: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb7b8b7ec>,
 5: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb7b8bdec>,
 6: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb7b873cc>,
 9: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb7b878ec>,
 10: <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb7b87e0c>,
...

unambiguous_dna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTableDNA i\
nstance at 0xb7b88aac>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTableDNA inst\
ance at 0xb7b8a12c>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTableDNA instance at 0xb7b\
883ac>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTableDNA in\
stance at 0xb7b8adac>,
...

unambiguous_rna_by_id

Type:
dict
Value:
{1: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb7890cec>,
 2: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb7b8b2ac>,
 3: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb7b8b7cc>,
 4: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb7b8bdcc>,
 5: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb7b873ac>,
 6: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb7b878cc>,
 9: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb7b87dec>,
 10: <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb7b8832c>,
...

unambiguous_rna_by_name

Type:
dict
Value:
{'Alternative Yeast Nuclear': <Bio.Data.CodonTable.NCBICodonTableRNA i\
nstance at 0xb7b8a0ac>,
 'Ascidian Mitochondrial': <Bio.Data.CodonTable.NCBICodonTableRNA inst\
ance at 0xb7b8a6ec>,
 'Bacterial': <Bio.Data.CodonTable.NCBICodonTableRNA instance at 0xb7b\
88a2c>,
 'Blepharisma Macronuclear': <Bio.Data.CodonTable.NCBICodonTableRNA in\
stance at 0xb7b9038c>,
...

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