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BackTranslate: Functions for reverse translation.

Project Description

# 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 ‘TTG’ into a stop codon. substitutions = bt.with_dna(‘TGG’, ‘*’)

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. substitutions = bt.without_dna(‘W’, ‘*’)

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

bt.improvable()

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

from backtranslate.util import subst_to_cds

# Transform the substitutions to CDS coordinates. variants = subst_to_cds(substitutions, 12)

## 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 …

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