Functions for reverse translation.
Switch branches/tags
Nothing to show
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
backtranslate
data
tests
.gitignore
.travis.yml
README.md
heatmap.ipynb
requirements.txt
setup.py

README.md

Back translation

This library provides functions for back translation from amino acids to nucleotides.

>>> from __future__ import unicode_literals
>>>
>>> from backtranslate.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: set([('G', 'A')]), 2: set([('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: set([('G', 'A')]), 2: set([('G', 'A')])}

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

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

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

>>> from backtranslate.util import subst_to_cds
>>>
>>> substitutions = bt.without_dna('W', '*')
>>>
>>> # Transform the substitutions to CDS coordinates.
>>> subst_to_cds(substitutions, 12)
set([(15, 'G', 'A'), (14, 'G', 'A')])

Command line interface

Use the command backtranslate to find substitutions that explain an amino acid change:

$ backtranslate with_dna -o 210 data/mhv.fa - 1 Leu
1       A       C
1       A       T

If no reference is available, use the without_dna subcommand:

$ backtranslate without_dna - Asp 92 Tyr
274     G       T

The command find_stops finds a list of positions and substitutions that lead to stop codons. This list of destructive substitutions are useful when analysing a pool of viral transcripts. Counting the appropriate nucleotides at the given positions gives insight into how many transcripts are active.

$ backtranslate find_stops -o 210 data/mhv.fa -
216     A       T
225     A       T
230     C       A
230     C       G
243     A       T
...