I recently finished another assignment for my Intro to Bioinformatics class at LTU. This one is a Python 2.7 program which uses dynamic programming to perform semi-global alignments on genetic sequences. The algorithm used is based on the Needleman-Wunsch algorithm.
An illustration of the Needleman-Wunsch algorithm from Wikipedia.

I find the most interesting part of my solution is that it generates its output as an HTML file with embedded JavaScript. This shows both the dynamic programming table used to generate the alignments, as well as the alignments themselves. The program will ask if you want to open it in your web browser, where you will also see a button to print the output if you want.

This code is not without its problems, especially given that I was short on time when I made my submission. It might have some performance issues, especially on longer input sequences. The alignments might scroll off the right side of the page. There doesn't seem to be any serious bugs though, and it gets the alignments right at any rate, even if it might take a little bit.

If you're curious about it, you can check it out on GitHub.


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