Bioinformatics with Python Cookbook

Chapter 3. Working with Genomes

In this chapter, we will cover the following recipes:

• Working with high-quality reference genomes
• Dealing with low-quality reference genomes
• Traversing genome annotations
• Extracting genes from a reference using annotations
• Finding orthologues using the Ensembl REST API
• Retrieving gene ontology information from Ensembl

Introduction

Many tasks in computational biology are dependent on the existence of reference genomes. If you are performing a sequence alignment, finding genes, or studying genetics of populations at several points of your work, you will be directly or indirectly using a genome reference. In this chapter, we will develop some recipes to work with reference genomes and deal with varying quality of references ...