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The Bio.Data.CodonTable module provides genetic code tables from the NCBI, used for translating nucleotide sequences to proteins.

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Overview

Biopython includes all NCBI genetic code tables, supporting both DNA and RNA sequences, with ambiguous and unambiguous variants. 
from Bio.Data import CodonTable

# Standard genetic code (Table 1)
standard_table = CodonTable.standard_dna_table
print(standard_table.forward_table['ATG'])  # 'M'
print(standard_table.stop_codons)           # ['TAA', 'TAG', 'TGA']

# Access by ID
table = CodonTable.unambiguous_dna_by_id[1]

# Access by name
table = CodonTable.unambiguous_dna_by_name['Standard']

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CodonTable Class

Base class representing a codon table or genetic code.

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Attributes

  • forward_table - dict[str, str] - Maps codons to amino acids
  • back_table - dict[str, str] - Maps amino acids to codons (for back-translation)
  • start_codons - list[str] - List of valid start codons
  • stop_codons - list[str] - List of stop codons
  • nucleotide_alphabet - str | None - Nucleotide alphabet (DNA/RNA)
  • protein_alphabet - str | None - Protein alphabet

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Methods

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__init__()

CodonTable(
    nucleotide_alphabet: str | None = None,
    protein_alphabet: str | None = None,
    forward_table: dict[str, str] = {},
    back_table: dict[str, str] = {},
    start_codons: list[str] = [],
    stop_codons: list[str] = []
) -> None
Initialize a codon table.

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__str__()

Returns a formatted text representation of the codon table. 
print(CodonTable.standard_dna_table)
# Table 1 Standard, SGC0
# 
#   |  T      |  C      |  A      |  G      |
# --+---------+---------+---------+---------+--
# T | TTT F   | TCT S   | TAT Y   | TGT C   | T
# T | TTC F   | TCC S   | TAC Y   | TGC C   | C
# ...

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NCBICodonTable Classes

Specialized classes for NCBI genetic code tables.

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NCBICodonTable

Base class for generic nucleotide sequences (accepts both DNA and RNA). Attributes:
  • id - int - NCBI genetic code ID
  • names - list[str] - List of names for this table

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NCBICodonTableDNA

Codon table for unambiguous DNA sequences. Attributes:
  • nucleotide_alphabet - Set to IUPACData.unambiguous_dna_letters

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NCBICodonTableRNA

Codon table for unambiguous RNA sequences. Attributes:
  • nucleotide_alphabet - Set to IUPACData.unambiguous_rna_letters

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AmbiguousCodonTable

Codon table supporting ambiguous nucleotide codes. 
from Bio.Data import CodonTable

table = CodonTable.ambiguous_dna_by_id[1]
print(table.forward_table['ATG'])  # 'M'
print(table.forward_table['ATR'])  # 'M' (R = A or G, so ATR = ATA or ATG)

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Table Dictionaries

Tables are accessible via dictionaries by ID or name:

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By ID

  • unambiguous_dna_by_id - DNA tables (unambiguous)
  • unambiguous_rna_by_id - RNA tables (unambiguous)
  • generic_by_id - Generic nucleotide tables (DNA or RNA)
  • ambiguous_dna_by_id - DNA tables with ambiguity codes
  • ambiguous_rna_by_id - RNA tables with ambiguity codes
  • ambiguous_generic_by_id - Generic tables with ambiguity codes

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By Name

  • unambiguous_dna_by_name - DNA tables by name
  • unambiguous_rna_by_name - RNA tables by name
  • generic_by_name - Generic tables by name
  • ambiguous_dna_by_name - Ambiguous DNA tables by name
  • ambiguous_rna_by_name - Ambiguous RNA tables by name
  • ambiguous_generic_by_name - Ambiguous generic tables by name

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Standard Tables

  • standard_dna_table - The standard genetic code (ID 1) for DNA
  • standard_rna_table - The standard genetic code (ID 1) for RNA

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Common Genetic Codes

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Table 1: Standard

table = CodonTable.unambiguous_dna_by_id[1]
# Names: ['Standard', 'SGC0']
# Start codons: ['TTG', 'CTG', 'ATG']
# Stop codons: ['TAA', 'TAG', 'TGA']

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Table 2: Vertebrate Mitochondrial

table = CodonTable.unambiguous_dna_by_id[2]
# Start codons: ['ATT', 'ATC', 'ATA', 'ATG', 'GTG']
# Stop codons: ['TAA', 'TAG', 'AGA', 'AGG']
# TGA codes for Trp (W) instead of stop
# ATA codes for Met (M) instead of Ile

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Table 11: Bacterial, Archaeal and Plant Plastid

table = CodonTable.unambiguous_dna_by_id[11]
# Start codons: ['TTG', 'CTG', 'ATT', 'ATC', 'ATA', 'ATG', 'GTG']
# Stop codons: ['TAA', 'TAG', 'TGA']

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Exceptions

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TranslationError

from Bio.Data.CodonTable import TranslationError
Raised when translation-specific errors occur, such as:
  • Invalid codon encountered
  • Ambiguous codon with no unique translation

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Example Usage

from Bio.Data import CodonTable

# Get the standard genetic code
table = CodonTable.standard_dna_table

# Translate a codon
codon = 'ATG'
amino_acid = table.forward_table[codon]
print(f"{codon} -> {amino_acid}")  # 'ATG -> M'

# Check if codon is a start codon
if codon in table.start_codons:
    print(f"{codon} is a start codon")

# Check if codon is a stop codon
if codon in table.stop_codons:
    print(f"{codon} is a stop codon")

# Use mitochondrial code
mito_table = CodonTable.unambiguous_dna_by_id[2]
print(mito_table.forward_table['TGA'])  # 'W' (Trp in mito code)

# Work with ambiguous codons
ambig_table = CodonTable.ambiguous_dna_by_id[1]
try:
    aa = ambig_table.forward_table['NNN']  # N = any base
except CodonTable.TranslationError:
    print("No unique amino acid for this codon")

# List all available tables
for table_id in sorted(CodonTable.unambiguous_dna_by_id.keys()):
    table = CodonTable.unambiguous_dna_by_id[table_id]
    print(f"Table {table_id}: {table.names[0]}")

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See Also

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