Let’s take a look at how we can program a Hamming Distance algorithm in three different ways — We can use Hamming Distance to measure/count nucleotide differences in DNA/RNA. This is very useful when we are searching for a particular pattern in a genome with up to n mutations. …

DNA Engine project structure and class setup. — In this article, will focus purely on laying out the structure for our ‘DNA Engine’ project. We will start adding elements and programming them in our next article. So here is the structure we had up and running last time (Test UI and a Test Class):

Python dictionary, Rust HashMap and a DNA Reverse Complement function — In our last article, we looked at how we can use Strings in Rust to store Genome data (DNA sequences). We will be using Strings extensively in our future code, as they are very convenient when it comes to storing and manipulating DNA/RNA data. In this article, we are taking…

Strings, Functions, and Crates/Modules — In our “dna_toolkit” series, we used Python Strings, Lists, and Dictionaries extensively. These data structures are very useful and make our life very easy. Let’s see what Rust has to offer. We start with Strings. Rust has two types. One, called 'String slice', and the other one is more like…

In Part 1 we look at PyQt setup, Qt Designer, UI converter tool and write a test application. — Hello and welcome to “Bioinformatics Tools Programming in Python with Qt“ article/video series. In this series, we will start developing a Qt framework based application using Python programming language. Qt is a free and open-source widget toolkit for creating graphical user interfaces as well as cross-platform applications that run on…

In this series of articles, we will explore a young and very exciting programming language — Rust. We will see how Rust can help us to speed up some of our existing and future Python code. Many agree, that the key features of Python are its simplicity and readability. …

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 will help us to search for proteins in DNA sequences by generating reading frames. …

Before we take a look at a Translation function, we need to create a structure to hold the DNA/RNA codon table. We will use a Python dictionary as it is just perfect for holding multiple keys, that have the same value. Let’s add this to our structures.py file:

In this article, we are going to implement two functions. The first function will count G and C nucleotides (GC Content) in a string, and the second function will use the first function but allow us to specify a ‘window’ size to calculate GC content in. Here is a Wikipedia…