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. In biology the genome of an organism is the whole hereditary information of an organism that is encoded in the DNA (or, for some viruses, RNA). ... In biology, a species is one of the basic units of biodiversity. ... In biology, Strain can be used two ways. ... A gigabyte (derived from the SI prefix giga-) is a unit of information or computer storage equal to one billion (short scale) bytes or 230 bytes (1024 mebibytes)[1]. It is commonly abbreviated GB (not to be confused with Gb, which is used for gigabits). ... Gene finding is the area of computational biology that is concerned with algorithmically identifying stretches of sequence, usually genomic DNA, that are biologically functional. ...

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). A representation of the 3D structure of myoglobin, showing coloured alpha helices. ... Ribonucleic acid or RNA is a nucleic acid polymer consisting of nucleotide monomers that plays several important roles in the processes that translate genetic information from deoxyribonucleic acid (DNA) into protein products; RNA acts as a messenger between DNA and the protein synthesis complexes known as ribosomes, forms vital portions... In biochemistry, a regulatory region is a DNA base sequence that controls gene expression. ... This article or section does not cite any references or sources. ... In biology, a species is one of the basic units of biodiversity. ... Stabilizing selection, also known as purifying selection or negative selection, is a type of natural selection in which genetic diversity decreases as the population stabilizes on a particular trait value. ... In population genetics, directional selection (sometimes referred to as positive selection) occurs when natural selection favors a single allele and therefore allele frequency continuously shift in one direction. ...

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. A model organism is one that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the model organism will provide insight into the workings of other organisms. ... Typical divisions Ascomycota (sac fungi) Saccharomycotina (true yeasts) Taphrinomycotina Schizosaccharomycetes (fission yeasts) Basidiomycota (club fungi) Urediniomycetes Sporidiales Yeasts are a growth form of eukaryotic microorganisms classified in the kingdom Fungi. ...

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. In biochemistry, a regulatory region is a DNA base sequence that controls gene expression. ... Small interfering RNA (siRNA) are a class of 20-25 nucleotide-long RNA molecules that interfere with the expression of genes. ... The structure of part of a DNA double helix Deoxyribonucleic acid (DNA) is a nucleic acid that contains the genetic instructions for the development and function of living organisms. ...

Computational approaches to genome comparison have recently become a common research topic in computer science. The development of computer-assisted mathematics (using products such as Mathematica or Matlab) has helped engineers, mathematicians and computer scientists to start operating in this domain, and a public collection of case studies and demonstrations is growing, ranging from whole genome comparisons to gene expression analysis. ^[1]. This has increased the introduction of different ideas, including concepts from systems and control, information theory, strings analysis and data mining. It is anticipated that computational approaches will become and remain a standard topic for research and teaching, while students fluent in both topics start being formed in the multiple courses created in the past few years. Mathematica is a general computing environment, organizing many algorithmic, visualization, and user interface capabilities within a document-like user interface paradigm. ... MATLAB is a numerical computing environment and programming language. ...

See also

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

This article is about evolution in biology. ... Molecular evolution is the process of the genetic material in populations of organisms changing over time. ... In population genetics, genetic drift is the statistical effect that results from the influence that chance has on the success of alleles (variants of a gene). ... This article or section does not cite any references or sources. ... The molecular clock (based on the molecular clock hypothesis (MCH)) is a technique in genetics, which researchers use to date when two species diverged. ... This article or section does not cite any references or sources. ... Comparative anatomy is the study of similarities and differences in the anatomy of organisms. ... A model organism is a species that is extensively studied to understand particular biological phenomena, with the expectation that discoveries made in the organism model will provide insight into the workings of other organisms. ...

References

1. ^ Cristianini, N. and Hahn, M. Introduction to Computational Genomics, Cambridge University Press, 2006. (ISBN-13: 9780521671910 | ISBN-10: 0521671914)

• Kellis M, Patterson N, Endrizzi M, Birren B, Lander E (2003). Sequencing and Comparison of yeast species to identify genes and regulatory elements. Nature, pp. 241-254 (15 May 2003).
• Cliften P, Sudarsanam P, Desikan A (2003). Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science, pp. 71-76 (4 July 2003).
• Hardison RC. (2003). Comparative genomics. PLoS biology, 1(2):e58.
• Stein LD, et al. (2003). The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biology, 1(2):E45. doi: 10.1371/journal.pbio.0000045
• Boffeli D, McAuliffe J, Ovcharenko D, Lewis KD, Ovcharenko I, Pachter L, Rubin EM (2003). Phylogenetic shadowing of primate sequences to find functional regions of the human genome, Science, 299(5611):1391-1394.
• Dujon B, et al. (2004). Genome evolution in yeasts. Nature, 430:35-44 (1 July 2004).
• Filipski A, Kumar S (2005). Comparative genomics in eukaryotes. In The Evolution of the Genome (ed. T.R. Gregory), pp. 521-583. Elsevier, San Diego.
• Gregory TR, DeSalle R (2005). Comparative genomics in prokaryotes. In The Evolution of the Genome (ed. T.R. Gregory), pp. 585-675. Elsevier, San Diego.
• Xie X, Lu J. Kulbokas EJ, Golub T, Mootha V, Lindblad-Toh K, Lander E, Kellis M (2005). Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature.
• Champ PC, Binnewies TT, Nielsen N, Zinman G, Kiil K, Wu H, Bohlin J, Ussery DW (2006). Genome update: purine strand bias in 280 bacterial chromosomes. Microbiology, 152(3):579-583. HubMed

Nature is one of the most prominent scientific journals, first published on 4 November 1869. ... Science is the journal of the American Association for the Advancement of Science (AAAS). ... The Public Library of Science (PLoS) is a nonprofit open access scientific publishing project aimed at creating a library of scientific journals and other scientific literature under an open content license. ... The Public Library of Science (PLoS) is a nonprofit open access scientific publishing project aimed at creating a library of scientific journals and other scientific literature under an open content license. ... Science is the journal of the American Association for the Advancement of Science (AAAS). ... Nature is one of the most prominent scientific journals, first published on 4 November 1869. ... // Summary The Evolution of the Genome is a book edited by Dr. T. Ryan Gregory of the University of Guelph, Ontario, Canada, covering a wide range of topics in the study of genome evolution. ... // Summary The Evolution of the Genome is a book edited by Dr. T. Ryan Gregory of the University of Guelph, Ontario, Canada, covering a wide range of topics in the study of genome evolution. ... Nature is one of the most prominent scientific journals, first published on 4 November 1869. ...

External links

• 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.