Genetic Code (`skbio.core.genetic_code`)¶

This module defines the GeneticCode class, which represents an immutable object that translates RNA or DNA strings to amino acid sequences.

Classes¶

GeneticCode(code_sequence[, id, name, ...]) Class to hold codon to amino acid mapping, and vice versa.

Examples¶

Creating and using a GeneticCode object

>>> from skbio.core.genetic_code import GeneticCodes
>>> from pprint import pprint
>>> sgc = GeneticCodes[1]
>>> sgc
GeneticCode(FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG)
>>> sgc['UUU'] == 'F'
True
>>> sgc['TTT'] == 'F'
True
>>> sgc['F'] == ['TTT', 'TTC']          #in arbitrary order
True
>>> sgc['*'] == ['TAA', 'TAG', 'TGA']   #in arbitrary order
True

Retrieving the anticodons of the object

>>> pprint(sgc.anticodons)
{'*': ['TTA', 'CTA', 'TCA'],
 'A': ['AGC', 'GGC', 'TGC', 'CGC'],
 'C': ['ACA', 'GCA'],
 'D': ['ATC', 'GTC'],
 'E': ['TTC', 'CTC'],
 'F': ['AAA', 'GAA'],
 'G': ['ACC', 'GCC', 'TCC', 'CCC'],
 'H': ['ATG', 'GTG'],
 'I': ['AAT', 'GAT', 'TAT'],
 'K': ['TTT', 'CTT'],
 'L': ['TAA', 'CAA', 'AAG', 'GAG', 'TAG', 'CAG'],
 'M': ['CAT'],
 'N': ['ATT', 'GTT'],
 'P': ['AGG', 'GGG', 'TGG', 'CGG'],
 'Q': ['TTG', 'CTG'],
 'R': ['ACG', 'GCG', 'TCG', 'CCG', 'TCT', 'CCT'],
 'S': ['AGA', 'GGA', 'TGA', 'CGA', 'ACT', 'GCT'],
 'T': ['AGT', 'GGT', 'TGT', 'CGT'],
 'V': ['AAC', 'GAC', 'TAC', 'CAC'],
 'W': ['CCA'],
 'Y': ['ATA', 'GTA']}