Technical requirements

In this chapter, we’ll use the following tools and packages:

• BioPython
• COBRApy
• ViennaRNA
• Entrez
• Prodigal
• HMMER

You’ll be instructed on how to install the relevant tools in each Getting ready section. The code for this chapter can be found at https://github.com/PacktPublishing/Bioinformatics-with-Python-Cookbook-Fourth-Edition/tree/main/Ch12.

You will want to create a Ch12 folder and set up your notebooks there.

Remember to activate your conda environment before beginning the recipes, like this:

conda activate bioinformatics_base

If you would like to set up a conda environment specific to this chapter, before activating bioinformatics_base, run the following:

conda create -n ch12-applications --clone bioinformatics_base
conda activate ch12-applications

You will be able to install the packages for the chapter as you go, or you can use the YAML file provided in the repository to set up the environment...