Genomics

From DrugPedia: A Wikipedia for Drug discovery

The goal of Genomics is to promote the understanding of the structure, function, and evolution of genomes in all kingdoms of life and the application of genome sciences and technologies to challenging problems in biology and medicine.

• Comparative genomics analysis that yields valuable insights into conserved and divergent aspects of function, regulation, and evolution.Comparative genomics is the analysis and comparison of genomes from different species. The purpose is to gain a better understanding of how species have evolved and to determine the function of genes and noncoding regions of the genome. Researchers have learned a great deal about the function of human genes by examining their counterparts in simpler model organisms such as the mouse. Genome researchers look at many different features when comparing genomes: sequence similarity, gene location, the length and number of coding regions (called exons) within genes, the amount of noncoding DNA in each genome, and highly conserved regions maintained in organisms as simple as bacteria and as complex as humans.

organism estimated size(base pairs) estimatedgene number average gene density chromosome number Homo sapiens (human) 3.2 billion ~25,000 1 gene per 100,000 bases 46

Mus musculus (mouse) 2.6 billion ~25,000 1 gene per 100,000 bases 40

Drosophila melanogaster (fruit fly) 137 million 13,000 1 gene per 9,000 bases 8

Arabidopsis thaliana (plant) 100 million 25,000 1 gene per 4000 bases 10

Caenorhabditis elegans (roundworm) 97 million 19,000 1 gene per 5000 bases 12

Saccharomyces cerevisiae (yeast) 12.1 million 6000 1 gene per 2000 bases 32

Escherichia coli (bacteria) 4.6 million 3200 1 gene per 1400 bases 1

H. influenzae (bacteria) 1.8 million 1700 1 gene per 1000 bases 1

• Information extracted from genome publication papers below.

Comparative genomics involves the use of computer programs that can line up multiple genomes and look for regions of similarity among them. Some of these sequence-similarity tools are accessible to the public over the Internet. One of the most widely used is BLAST, which is available from the National Center for Biotechnology Information. BLAST is a set of programs designed to perform similarity searches on all available sequence data. For instructions on how to use BLAST, see the tutorial Sequence similarity searching using NCBI BLAST available through Gene Gateway, an online guide for learning about genes, proteins, and genetic disorders. Functional genomics approaches involving the use of large-scale and/or high-throughput methods to understand genome-scale function and regulation of transcriptomes and proteomes.The implications of functional genomics research are particularly important in healthcare, from greater disease understanding to predictions, novel therapies and new opportunities for industry; in addition there are environmental implications, while ethical and legal issues are of increasing public interest and concern.The first area of focus is on leading-edge technology development in arrays, nanosystems, and gene silencing. Highly sensitive array systems (biochips) are being developed for genotyping, resequencing, transcriptome analysis, protein detection and function, and cell and tissue analysis, while nanosystems will allow for detection and analysis down to the single molecule and single cell levels. Mutational and knockdown strategies, particularly the powerful, recently introduced RNA interference (RNAi), can specifically silence individual genes, the phenotypic effects of which can be observed on a global scale in genetically amenable model organisms or cells. A second focus is on bioinformatics, without which the data cannot be made accessible, organised and understood, and systems biology. The latter, one of the most far-reaching developments in recent years, attempts to understand function not on individual genes or proteins but on multimolecular modules and ever more complex systems. Three levels of genomic analysis - the mRNA level, the protein level, and the level of low molecular weight intermediates (metabolites) - combine to provide an understanding of whole organism functioning. Systems biology aims to describe how the molecular properties of the cell constituents lead to its complex organisation and integrated properties, and beyond that to the predictable development of organs and the organism as a whole.

Structural genomics consists in the determination of the three dimensional structure of all proteins of a given organism, by experimental methods such as X-ray crystallography, NMR spectroscopy or computational approaches such as homology modelling.

Significant advances in genetic and genomics technologies and their applications, including chemical genomics