Alignment Beyond Sequences - Genomes is the tenth of 12 lectures on Biological Sequence Analysis [BSA], I give at ANU, Canberra, Australia in September to December 2018. BSA is a huge field since sequences are presently so abundant.
In this lecture we discuss comparison of overall genome structure (how to change gene order using inversions, duplications,..), genome alignment and the evolution of multigene families – all essential to genome analysis. This is quite a mouthful so it will be a summary of what is important within these sub-topics.
Genome Structure Alignment is important when you know the gene orders and orientation on a genome, then it can be valuable to transform one genome into another using specified operations. Or a set of genome structures can be known and related by a tree. This ignores the information at the sequence level, whole Genome Alignment will also align at the nucleotide level. At a finer level than whole genomes, but higher than sequence level we find the analysis of Multigene Families. Multigene Families are ubiquitous and pose the challenge to phylogenetics that you can infer (sometimes) the tree relating genes, but what you are after is the species phylogeny. Packing the gene tree inside the specie tree is called reconciliation and many algorithms have been devised for doing this.
Preliminary slides can be found here.