Introduction

Many tasks in computational biology are dependent on the existence of reference genomes. If you are performing sequence alignment, finding genes, or studying the genetics of populations, you will be directly or indirectly using a reference genome. In this chapter, we will develop some recipes for working with reference genomes and dealing with references of a varying quality—which can vary from high quality, as with the human genome, to problematic with non-model species. We will also look at how to deal with genome annotations (working with text databases that will point us to interesting features in the genome) and extract sequence data using the annotation information. We will also try to find some gene orthologues across species. Finally, we will access a Gene Ontology (GO) database.