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Comparative Genomics - Bioinformatics

Comparative Genomics Introduction

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.

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. 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.


Evolutionary Conserved Region Bioinformatics

Evolutionary Conserved Regions also called ECRs for short are regions of sequence (usually DNA) that have been mapped to align with other genomes and are conserved.

ECRs within alignments of the genomes are presented in this graphical browser, which depicts and color-codes ECRs in relation to known genes that have been annotated in the base genome. 'Grab ECR' feature allows users to rapidly extract sequences that correspond to any ECR, to visualize underlying sequence alignments and/or identify conserved transcription factor binding sites.


ECR Browser is a new dynamic whole-genome navigation tool for the visualization and study of evolutionary relationships between vertebrates and non-vertebrate genomes. ECR Browser is constantly being updated to include the most recently available sequenced genomes (currently: human, dog, mouse, rat, chicken, frog two pufferfish (Fugu and Tetraodon), zebrafish, and 6 fruitflies). Ovcharenko, M.A. Nobrega, G.G. Loots, and L. Stubbs ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes Nucleic Acids Research, 32, W280-W286 (2004)

ECRbase is the Database of Evolutionary Conserved Regions (ECRs), Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes created using ECR Browser alignments


Bioinformatics Forum

Discuss and post questions about protein expression in the Bioinformatics Forum.


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