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Concepts Summary

Genomics is the field of genetics that attempts to understand the content, organization, and function of genetic information contained in whole genomes.
Genetic maps position genes relative to other genes by determining rates of recombination and are measured in percent recombination. Physical maps are based on the physical distances between genes and are measured in base pairs.
The Human Genome Project was an effort to determine the entire sequence of the human genome. The project began officially in 1990; rough drafts of the human genome sequence were completed in 2000. The final draft of the human genome sequence was completed in 2003.
Sequencing a whole genome requires breaking it into small overlapping fragments whose DNA sequences can be determined in sequencing reactions. The individual sequences can be ordered into a whole-genome sequence using a map-based approach, in which fragments are assembled in order by using previously created genetic and physical maps, or with the use of a whole-genome shotgun approach, in which overlap between fragments is used to assemble them into a whole-genome sequence. Today, almost all genomes are sequenced using whole-genome shotgun sequencing.
Single-nucleotide polymorphisms are single-base differences in DNA between individual organisms and are valuable as markers in linkage studies. Individual organisms may also differ in the number of copies of DNA sequences, called copy-number variations.
Sequence-tagged sites are unique DNA sequences whose chromosomal location has been determined. Expressed-sequence tags are markers associated with expressed (transcribed) DNA sequences and can be used to find the genes expressed in a genome.
Bioinformatics is a synthesis of molecular biology and computer science that develops tools to store, retrieve, and analyze DNA-, cDNA-, and protein-sequence data.
Metagenomics studies the genomes of entire groups of organisms. Synthetic biology is developing techniques for creating genomes and organisms.
Homologous genes are evolutionarily related. Orthologs are homologous sequences found in different organisms, whereas paralogs are homologous sequences found in the same organism. Gene function may be determined by looking for homologous sequences (both orthologs and paralogs) whose function has been previously determined.
A microarray consists of DNA fragments fixed in an orderly pattern to a solid support, such as a nylon filter or glass slide. When a solution containing a mixture of DNA or RNA is applied to the array, any nucleic acid that is complementary to the probe being used will bind to the probe. Microarrays can be used to monitor the expression of thousands of genes simultaneously.
By linking a reporter sequence with the regulatory sequences of a gene, the expression pattern of the gene can be observed by looking for the product of the reporter sequence. Genes affecting a particular function can also be identified through whole-genome mutagenesis screens.
Most prokaryotic species have between 1 million and 3 million base pairs of DNA and from 1000 to 2000 genes. Compared with that of eukaryotic genomes, the density of genes in prokaryotic genomes is relatively uniform, with about one gene per 1000 bp. There is relatively little noncoding DNA between prokaryotic genes. Horizontal gene transfer (the movement of genes between different species) has been an important evolutionary process in prokaryotes.
Eukaryotic genomes are larger and more variable in size than prokaryotic genomes. There is no clear relation between organismal complexity and the amount of DNA or number of genes among multicellular organisms. Much of the genomes of eukaryotic organisms consist of repetitive DNA. Transposable elements are very common in most eukaryotic genomes.
Proteomics determines the protein content of a cell and the functions of those proteins. Proteins within a cell can be separated and identified with the use of mass spectrometry. Structural proteomics attempts to determine the three-dimensional shape of proteins.