Library

This library provides functions for back translation from amino acid changes to nucleotide changes.

>>> from mutalyzer_backtranslate import BackTranslate
>>>
>>> # Create a class instance, optionally giving the translation table id.
>>> bt = BackTranslate()
>>>
>>> # Find all substitutions that transform the codon 'TGG' into a stop codon.
>>> bt.with_dna('TGG', '*')
{1: {('G', 'A')}, 2: {('G', 'A')}}

Sometimes we do not have access to the DNA sequence so we have to find possible substitutions from the amino acids directly.

>>> # Find all substitutions that transform a Tryptophan into a stop codon.
>>> bt.without_dna('W', '*')
{1: {('G', 'A')}, 2: {('G', 'A')}}

To find out which substitution predictions can be improved by adding codon information, use the following function.

>>> bt.improvable()
{('N', 'K'), ('R', 'W'), ('L', 'F'), ('D', 'E'), ('E', 'D'), ('C', 'W'),
 ('K', 'N'), ('Q', 'H'), ('C', '*'), ('I', 'L'), ('G', 'R'), ('F', 'L'),
 ('S', '*'), ('T', 'S'), ('*', 'S'), ('S', 'R'), ('R', 'S'), ('V', 'L'),
 ('R', 'G'), ('Y', '*'), ('S', 'T'), ('*', 'L'), ('*', 'W'), ('H', 'Q'),
 ('L', 'I'), ('I', 'M'), ('L', 'V'), ('L', 'M'), ('L', '*'), ('R', '*'),
 ('S', 'C'), ('*', 'Y')}

To get substitutions in a readable format, we can use the following:

>>> from mutalyzer_backtranslate.util import subst_to_cds
>>>
>>> substitutions = bt.without_dna('W', '*')
>>>
>>> # Transform the substitutions to CDS coordinates.
>>> subst_to_cds(substitutions, 12)
{(14, 'G', 'A'), (15, 'G', 'A')}