DNA shuffling is a molecular biology technique used in directed evolution studies. The technique relies on the similarities between two or more DNA sequences. This program can be used to increase the similarities between two DNA sequences. After harmonization the two sequence can be shuffled together and screened for improved properties.
This code was inspired by the paper Shuffle Optimizer: A Program to Optimize DNA Shuffling for Protein Engineering written by John N. Milligan and Daniel J. Garry. However, the code below uses Python 3 and makes a few different codon choices. On the whole, the outputs should be largely the same.
Run code with:
# print sequences into the command prompt
python shuffle.py example_sequences.fna
# or wirte the outputs to a file
python shuffle.py example_sequences.fna > output.txt
This program uses the Biopython library. Go here for installation instructions before using the script.
MIT License
Copyright (c) [2017] [Jeremy LaBarge]
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