Read Alignment

Next let’s look at building a little more sophisticated example using ChatGPT. In this recipe we will write code to align two reads together, a common bioinformatics task.A core algorithm in bioinformatics is Alignment. This is the task of taking two or more sequences and seeing how the sequences can optimally line up with each other. Alignment is used in many bioinformatics tasks, for example to see how different species may relate to each other (phylogenetics), how proteins may have evolved, or to take many sequencing reads and align them to a reference to do variant calling.

How to do it...

Here are the steps to try this recipe:

1. Go into ChatGPT and get ready to give it the following prompt: Write an example that aligns two DNA sequences
2. This will write example code that uses Biopython’s Bio.Align module. The code will work; however, we notice that it uses the pairwise2 algorithm. When you paste this code into your notebook and run it, you will get a message...