6 - Whole Genome Alignment

Abstract

The methods described in the earlier parts of this book were generally developed to align sets of relatively short protein or RNA sequences. However, the availability of whole genome sequences has led to an interest in MSAs for complete genomes, often referred to as whole genome alignment (WGA). In this case, specialized alignment tools are needed. The first problem concerns the increased sequence lengths: single gene sequences may be as long as tens of thousands of nucleotides, but whole genomes are usually millions of nucleotides or larger. Apart from the increased size of the data, WGA methods also need to take into account more complex evolutionary events including genome rearrangements (inversions, translocations, chromosome fusions or fissions, etc.), in addition to substitutions and insertions/deletions. Some tools for WGA are also capable of modeling unbalanced rearrangements that lead to copy number changes, such as tandem and segmental duplications.