5.1: Introduction
- Page ID
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In the previous chapter, we saw the importance of comparative genomics analysis for discovering functional elements. In “part IV” of this book, we will see how we can use comparative genomics for studying gene evolution across species and individuals. In both cases however, we assumed that we had access to complete and aligned genomes across multiple species.
In this chapter, we will study the challenges of genome assembly and whole-genome alignment that are the foundations of whole-genome comparative genomics methodologies. First, we will study the core algorithmic principles underlying many of the most popular genome assembly methods available today. Second, we will study the problem of whole-genome alignment, which requires understanding mechanisms of genome rearrangement (e.g. segmental duplication and other translocations). The two problems of genome assembly and whole-genome alignment are similar in nature, and we close by discussing some of the parallels between them.
