ABSTRACT
Abstract Fast progress in human and other genome sequencing has created a foundation for global functional analysis of complex genomes. Genome-wide interindividual, population, and interspecies comparisons of genome variability and instability provide most valu-
able approaches for deciphering spatial and temporal regulatory networks. Importantly, comparative genomics allows also for studies of biological evolution. Genome-wide comparisons are also indispensable for understanding the genetic and environmental contributions to complex diseases affiicting modern society. In this review we discuss a variety of available approaches to genome-wide complex genome comparisons, their informativeness, advantages, and shoncomings. It is evident that new, more powerful methods are in critical demand for comprehensive comparisons of complex genomes.
