Bioinformatics with Python Cookbook - Second Edition

Extracting genes from a reference using annotations

In this recipe, we will look at how to extract a gene sequence with the help of an annotation file to get its coordinates against a reference FASTA. We will use the Anopheles gambiae genome, along with its annotation file (as per the previous two recipes). We will first extract the voltage-gated sodium channel (VGSC) gene, which is involved in resistance to insecticides.