In this article, we are going to take a look at one of the algorithms we wrote in Genome Toolkit series, Part 2, and attempt to optimize it.
Tag: Bioinformatics
In the previous article (Part 2 here), we wrote our first Genome Toolkit algorithm. Even though, it was a very simple algorithm to help us search for repeating patterns (k-mers) in a DNA/Genome sequences, and it seemed to worked correctly, we actually had a bug in it. Let’s take a look at what it is, and how we can fix it.
Bioinformatics with Python Cookbook: Use modern Python libraries and applications to solve real-world computational biology problems, 3rd Edition.
First function – counting patterns in a sequence.
Let’s look at how we can program Hamming Distance algorithm in three different ways.
In this article, we conclude our work on a minimal set of functions to work with DNA. We will add the last three functions that
In this article we are taking a look at DNA Codon table and adding a Translation and Codon Usage functions to our DNA Toolkit.
In this article we add GC Content Calculation functions to the DNA Toolkit
In this article we install and set-up VSCode/VSCodium editor and a few plugins to make running any code easy, with just a key combination.
Welcome back! Today we continue working on our DNA Toolkit project. In our last article, we created the first two functions: validate_seq and nucleotide_frequency. We