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Comparative genomics is the study of relationships between the genomes of different species or strains. Comparative genomics is an attempt to take advantage of the information provided by the signatures of selection to understand the function and evolutionary processes that act on genomes. While it is still a young field, it holds great promise to yield insights into many aspects of the evolution of modern species. The sheer amount of information contained in modern genomes (several gigabytes in the case of humans) necessitates that the methods of comparative genomics are mostly computational in nature. Gene finding is an important application of comparative genomics, as is discovery of new, non-coding functional elements of the genome.

Comparative genomics exploits both similarities and differences in the proteins, RNA, and regulatory regions of different organisms to infer how selection has acted upon these elements. Those elements that are responsible for similarities between different species should be conserved through time (stabilizing selection), while those elements responsible for differences among species should be divergent (positive selection). Finally, those elements that are unimportant to the evolutionary success of the organism will be unconserved (selection is neutral).

Identifying the mechanisms of eukaryotic genome evolution by comparative genomics is one of the important goals of the field. It is however often complicated by the multiplicity of events that have taken place throughout the history of individual lineages, leaving only distorted and superimposed traces in the genome of each living organism. For this reason comparative genomics studies of small model organisms (for example yeast) are of great importance to advance our understanding of general mechanisms of evolution.

Having come a long way from its initial use of finding functional proteins, comparative genomics is now concentrating on finding regulatory regions and siRNA molecules. Recently, it has been discovered that distantly related species often share long conserved stretches of DNA that do not appear to code for any protein. It is unknown at this time what function such ultra-conserved regions serve.

• Evolution
• Molecular evolution
• Genetic drift
• Selection
• Molecular clock
• Evolutionary biology
• Comparative anatomy
• Model organism

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• Genomes OnLine Database (GOLD)
• Genome News Network
• TIGR Comprehensive Microbial Resource
• CBS Genome Atlas Database
• The UCSC Genome Browser
• The U.S. National Human Genome Research Institute
• Ensembl The Ensembl Genome Browser
• Genolevures, comparative genomics of the Hemiascomycetous yeasts
• Phylogenetically Inferred Groups (PhIGs), a recently developed method incorporates phylogenetic signals in building gene clusters for use in comparative genomics.
• Metazome, a resource for the phylogenomic exploration and analysis of Metazoan gene families.
• IMG The Integrated Microbial Genomes system, for comparative genome analysis by the DOE-JGI.

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