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The Bio.Data module provides collections of biological data constants, including IUPAC alphabets, codon tables, and molecular weights.

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IUPACData

The Bio.Data.IUPACData module contains standard IUPAC definitions for biological alphabets and molecular weights.

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Protein Alphabets

from Bio.Data import IUPACData

# Standard protein letters (20 amino acids)
protein_letters = IUPACData.protein_letters
# 'ACDEFGHIKLMNPQRSTVWY'

# Extended protein letters (including ambiguity codes)
extended_protein_letters = IUPACData.extended_protein_letters
# 'ACDEFGHIKLMNPQRSTVWYBXZJUO'
Constants:
  • protein_letters - Standard 20 amino acid one-letter codes
  • extended_protein_letters - Includes B (Asx), X (unknown), Z (Glx), J (Xle), U (Sec), O (Pyl)
  • protein_letters_1to3 - Dictionary mapping 1-letter to 3-letter codes
  • protein_letters_3to1 - Dictionary mapping 3-letter to 1-letter codes
  • protein_letters_1to3_extended - Extended version with ambiguity codes
  • protein_letters_3to1_extended - Extended version with ambiguity codes

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Nucleotide Alphabets

# DNA alphabets
unambiguous_dna_letters = IUPACData.unambiguous_dna_letters  # 'GATC'
ambiguous_dna_letters = IUPACData.ambiguous_dna_letters      # 'GATCRYWSMKHBVDN'

# RNA alphabets
unambiguous_rna_letters = IUPACData.unambiguous_rna_letters  # 'GAUC'
ambiguous_rna_letters = IUPACData.ambiguous_rna_letters      # 'GAUCRYWSMKHBVDN'

# Ambiguous nucleotide values
ambiguous_dna_values = IUPACData.ambiguous_dna_values
# {'A': 'A', 'C': 'C', 'G': 'G', 'T': 'T', 'M': 'AC', 'R': 'AG', ...}

ambiguous_rna_values = IUPACData.ambiguous_rna_values
# {'A': 'A', 'C': 'C', 'G': 'G', 'U': 'U', 'M': 'AC', 'R': 'AG', ...}
Constants:
  • unambiguous_dna_letters - Four standard DNA bases
  • ambiguous_dna_letters - DNA with IUPAC ambiguity codes
  • unambiguous_rna_letters - Four standard RNA bases
  • ambiguous_rna_letters - RNA with IUPAC ambiguity codes
  • ambiguous_dna_values - Maps ambiguity codes to possible bases (DNA)
  • ambiguous_rna_values - Maps ambiguity codes to possible bases (RNA)
  • ambiguous_dna_complement - DNA complement with ambiguity codes
  • ambiguous_rna_complement - RNA complement with ambiguity codes

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Molecular Weights

# Protein weights (average masses)
protein_weights = IUPACData.protein_weights
# {'A': 89.0932, 'C': 121.1582, 'D': 133.1027, ...}

# Monoisotopic protein weights
monoisotopic_protein_weights = IUPACData.monoisotopic_protein_weights
# {'A': 89.047678, 'C': 121.019749, ...}

# DNA/RNA nucleotide weights
unambiguous_dna_weights = IUPACData.unambiguous_dna_weights
unambiguous_rna_weights = IUPACData.unambiguous_rna_weights

# Atomic weights
atom_weights = IUPACData.atom_weights
# {'H': 1.00794, 'C': 12.0107, 'N': 14.0067, 'O': 15.9994, ...}
Constants:
  • protein_weights - Average molecular weights of amino acids
  • monoisotopic_protein_weights - Monoisotopic weights of amino acids
  • extended_protein_values - Maps ambiguous protein codes to possibilities
  • unambiguous_dna_weights - Weights of DNA nucleotides (monophosphate deoxy)
  • unambiguous_rna_weights - Weights of RNA nucleotides (monophosphate)
  • monoisotopic_unambiguous_dna_weights - Monoisotopic DNA weights
  • monoisotopic_unambiguous_rna_weights - Monoisotopic RNA weights
  • atom_weights - Atomic weights for elements

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PDBData

The Bio.Data.PDBData module contains protein structure-specific data from the wwPDB. 
from Bio.Data import PDBData

# Extended 3-to-1 letter protein code mapping (includes modified residues)
protein_letters_3to1_extended = PDBData.protein_letters_3to1_extended
# {'ALA': 'A', 'CYS': 'C', 'MSE': 'M', 'SEP': 'S', ...}

protein_letters_1to3 = PDBData.protein_letters_1to3
# {'A': 'ALA', 'C': 'CYS', 'D': 'ASP', ...}
Constants:
  • protein_letters_3to1 - Standard 3-to-1 letter mapping (uppercase)
  • protein_letters_1to3 - Standard 1-to-3 letter mapping
  • protein_letters_3to1_extended - Includes modified/non-standard amino acids

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Example Usage

from Bio.Data import IUPACData, PDBData

# Calculate molecular weight of a peptide
peptide = "ACDEFGH"
weight = sum(IUPACData.protein_weights[aa] for aa in peptide)
print(f"Peptide weight: {weight:.2f} Da")

# Decode ambiguous DNA
ambiguous_codon = "ATR"  # R = A or G
possible_bases = IUPACData.ambiguous_dna_values['R']
print(f"R can be: {possible_bases}")  # 'AG'

# Convert protein codes
three_letter = "MSE"  # Modified methionine
if three_letter in PDBData.protein_letters_3to1_extended:
    one_letter = PDBData.protein_letters_3to1_extended[three_letter]
    print(f"{three_letter} -> {one_letter}")  # 'M'

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See Also

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