TurtleAlign is a functional Python implementation of the much beloved Needleman–Wunsch Global alignment algorithm. This code is meant for educational purposes, namely to gain a deeper insight into sequence bioinformatics. If you plan on using this to align actual long gene sequences, bring with you a cup of coffee and plenty of patience.

TurtleAlign is a tool to visualize how two sequences align given a match score, a gap and a mismatch penalty.

TurtleAlign supports command line functionality, argument parsing and outputs the alignment in a txt file. To visualize the resulting txt file, make sure to disable line wrapping. For more information, run the './TurtleAlign.py -h' command in your terminal

The code comes with two bacterial gene fasta files to allow for illustration (I picked some very short ones on purpose, do not worry).

DNA1: First positional argument, takes a DNA sequence directly in the terminal or a DNA fasta file.

DNA2: Second positional argument, takes a DNA sequence directly in the terminal or a DNA fasta file.

-o, --out: Output file name

-m, --mat: Positive score for base pair match. Strictly positive integer value

-n, -mis: Negative score for base pair mismatch. Strictly negative integer value

-g, --gap: Negative score for the insertion of a gap. Strictly inferior to -1

Open the command line terminal and navigate to the TurtleAlign directory

First, ensure installation of the necessary packages: pip install -r requirements.txt

Run the following command and open the outputed txt file (named alignment_output.txt by default): ./TurtleAlign.py -m 2 -n -1 -g -2 MTuber_atpE.fasta EColi_atpE.fasta

If the txt file looks funny, disable line wrapping in the settings of your text editor and scroll along the sequence from end to end.

Unit tests have been added for all functions in case new features are added. If features are added and functions changed, make sure to run pytest -xv TurtleAlign.py to verify that existing functions work as intended. To ensure that the overall code runs and fails gracefully, navigate inside the tests directory and run pytest:

cd tests pytest -xv TurtleAlign_tests.py

The tests will fail unless you are in the tests directory when you run the pytest command.

Tests can be added or modified accordingly, as new features are added.