Module CodonTable

source code

Codon tables based on those from the NCBI.

These tables are based on parsing the NCBI file: ftp://ftp.ncbi.nih.gov/entrez/misc/data/gc.prt

Last updated for Version 3.9

Classes

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TranslationError

CodonTable

NCBICodonTable

NCBICodonTableDNA

NCBICodonTableRNA

AmbiguousCodonTable

AmbiguousForwardTable

Functions

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make_back_table(table, default_stop_codon)

source code

register_ncbi_table(name, alt_name, id, table, start_codons, stop_codons)

source code

list_possible_proteins(codon, forward_table, ambiguous_nucleotide_values)

source code

list_ambiguous_codons(codons, ambiguous_nucleotide_values)
Extends a codon list to include all possible ambigous codons.

source code

Variables

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unambiguous_dna_by_name = {}

unambiguous_dna_by_id = {}

unambiguous_rna_by_name = {}

unambiguous_rna_by_id = {}

generic_by_name = {}

generic_by_id = {}

ambiguous_generic_by_name = {'Alternative Flatworm Mitochondri...

ambiguous_generic_by_id = {}

standard_dna_table = None

standard_rna_table = None

ambiguous_dna_by_name = {}

ambiguous_dna_by_id = {}

ambiguous_rna_by_name = {}

ambiguous_rna_by_id = {}

__package__ = 'Bio.Data'

Function Details

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list_ambiguous_codons(codons, ambiguous_nucleotide_values)

source code

Extends a codon list to include all possible ambigous codons.

e.g. ['TAG', 'TAA'] -> ['TAG', 'TAA', 'TAR']
     ['UAG', 'UGA'] -> ['UAG', 'UGA', 'URA']

Note that ['TAG', 'TGA'] -> ['TAG', 'TGA'], this does not add 'TRR'.
Thus only two more codons are added in the following:

e.g. ['TGA', 'TAA', 'TAG'] -> ['TGA', 'TAA', 'TAG', 'TRA', 'TAR']

Returns a new (longer) list of codon strings.

Variables Details

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ambiguous_generic_by_name

Value:

{}