1. Genomics is an interdisciplinary field of science within the field of
Genomics is an interdisciplinary field of science within the field of molecular biology.
A genome is a complete set of DNA within a single cell of an organism, and as such, focuses on the structure, function, evolution, and mapping of genomes.
Genomics aims at the collective characterization and quantification of genes, which direct the production of proteins with the assistance of enzymes and messenger molecules.
Genomics also involves the sequencing and analysis of genomes.

2. INTRODUCTION
The term genome refers to the total genetic composition of an organism
The term genomics refers to the molecular analysis of the entire genome of a species
Genome analysis consists of two main phases
Mapping
Sequencing
In 1995, researchers led by Craig Venter and Hamilton Smith obtained the first complete DNA sequence of an organism
The bacterium Haemophilus influenzae
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3. The International Human Genome Sequencing Consortium published the first draft of the human genome in the journal Nature in February 2001 with the sequence of the entire genome's three billion base pairs some 90 percent complete.
A startling finding of this first draft was that the number of human genes appeared to be significantly fewer than previous estimates, which ranged from 50,000 genes to as many as 140,000.
The full sequence was completed and published in April 2003.

4. Genomics begins with the mapping of the genome and progresses ultimately to its complete sequencing
Functional genomics examines how the interactions of genes produces the traits of an organism
Proteomics is the study of all the proteins encoded by the genome and their interactions
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5. CHROMOSOME MAPPING
There are three common ways to determine the organization of DNA regions
1. Cytogenetic mapping
Relies on microscopy
Genes are mapped relative to band locations
Linkage mapping
Relies on genetic crosses
Genes are mapped relative to each other
Distances computed in map units (or centiMorgans)
3. Physical mapping
Relies on DNA cloning techniques
Distances computed in number of base pairs
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6. and from one region of the chromosome to another
Note: Correlations between the three maps often vary from species to species
and from one region of the chromosome to another
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7. Cytogenetic mapping relies on microscopy
It is commonly used with eukaryotes which have much larger chromosomes
Eukaryotic chromosomes can be distinguished by
Size
Centromeric locations
Banding patterns
Chromosomes are treated with particular dyes
The banding pattern that results is used for mapping
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8. In situ Hybridization
In situ hybridization can locate the position of a gene at a particular site within an intact chromosome
It is used to map the locations of genes or other DNA sequences within large eukaryotic chromosomes
a probe is used to detect the “target” DNA - fluorescence in situ hybridization (FISH).
To detect the light emitted by a fluorescent probe, a fluorescence microscope is used
The fluorescent probe will be seen as a colorfully glowing region against a nonglowing background
The results of the FISH experiment are then compared to Giemsa-stained chromosomes
Thus, the location of a probe can be mapped relative to the G banding pattern
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9. fluorescence in situ hybridization (FISH).

10. Linkage Mapping
Linkage mapping relies on the frequency of recombinant offspring to map genes
Even regions of DNA, which need not encode genes, can be used as genetic markers
A molecular marker is a DNA segment that is found at a specific site and can be uniquely recognized
As with alleles, the characteristics of molecular markers may vary from individual to individual (polymorphic)
Therefore, the distance between linked molecular markers can be determined from the outcome of crosses
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11. The amplified region is called a sequence-tagged site (STS)
The two STS copies in this case are different in length
Therefore, their microsatellites have different numbers of CA repeats

12. PHYSICAL MAPPING
Physical mapping requires the cloning of many pieces of chromosomal DNA
The cloned DNA fragments are then characterized by
1. Size
2. Genes they contain
3. Relative locations along a chromosome
Eukaryotic genomes are very large
Physical mapping will require many much smaller pieces
Will require a massive, collaborative undertaking
In recent years, physical mapping studies have led to the DNA sequencing of entire genomes
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13. The goal of functional genomics is to elucidate the roles of genetic sequences in a given species
In most cases, it aims to understand gene function
Transcriptomics is the study of the transcriptome—the complete set of RNA transcripts that are produced by the genome, under specific circumstances or in a specific cell—using high-throughput methods, such as microarray analysis.
The entire collection of proteins that an organism can make is termed the proteome
The goal of proteomics is to understand the functional roles of the proteins of a species
It aims to understand the interplay among proteins
The goal of bioinformatics is to extract information within genetic sequences using a mathematical/computational approach
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14. Expressed Genes Can be Identified in a cDNA Library
A basic goal of genomic research is to identify regions of DNA that actually encode genes
One way to do this, is to show that a given region is transcribed into RNA
This can be accomplished by the generation of a cDNA library
A cDNA library is also called an expressed sequence tag library (EST library)
Because the sequences are from expressed sequences and can also be used as markers (tags) in physical mapping studies
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15. A Microarray Can Identify Genes That Are Transcribed
Researchers have developed an exciting technology called DNA microarrays (also called gene chips)
This new technology makes it possible to monitor thousands of genes simultaneously
A DNA microarray is a small silica, glass or plastic slide that is dotted with many sequences of DNA
Each of these sequences corresponds to a known gene
These fragments are made synthetically
These sequences of DNA will act as probes to identify genes that are transcribed
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16. The DNA fragments can be either/or
Amplified by PCR and then spotted on the microarray
Synthesized directly on the microarray itself
A single slide contains tens of thousands of different spots in an area the size of a postage stamp
The relative location of each spot is known
The technology for making DNA microarrays is quite amazing
It involves spotting technologies that are quite similar to the way that an inkjet printer works
Once a DNA microarray has been made, it is used as a hybridization tool
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17. It is then placed in a scanning confocal fluorescence microscope
Array is washed
It is then placed in a scanning confocal fluorescence microscope
The pattern of fluorescence is analyzed to indicate hybridization
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18. Development of novel high-throughput DNA sequencing methods has provided a new method for both mapping and quantifying transcriptomes.
This method, termed RNA-Seq (RNA sequencing), has clear advantages over existing approaches and is expected to revolutionize the manner in which eukaryotic transcriptomes are analyzed.

19. PROTEOMICS
Proteomics examines the functional roles of the proteins that a species can make
The entire collection of a species’ proteins is its proteome
Genomic data can provide important information about the proteome
1. DNA microarrays reveal the genes that are transcribed under a given set of conditions
2. Gene homology studies between species can be used to predict protein structure and/or function
Genomic insights, however, have to be followed up with research that involves protein analysis directly
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20. The Proteome Is Much Larger Than the Genome
Sequencing and analysis of an entire genome can identify all the genes that a given species contains
The proteome is larger, however, and its actual size is more difficult to determine
This larger size is rooted in a number of cellular processes
1. Alternative splicing
2. RNA editing
3. Postranslational covalent modification
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21. Two-Dimensional Gel Electrophoresis
Any given cell of a multicellular organism will produce only a subset of the proteins in its proteome
The subset that it makes depends primarily on the
Cell type
Stage of development
Environmental conditions
A common technique in the field of proteomics is two-dimensional gel electrophoresis
It is a separation technique that can distinguish hundreds or even thousands of different proteins in a cell extract
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22. As the name suggests, the technique involves two different gel electrophoresis experiments. The first separates by pH/charge interactions, the second by size.
After the slab gel has run, the proteins within the gel can be stained with a dye
The end result is a collection of spots, with each spot corresponding to a unique cellular protein
This method can resolve two proteins that differ by a single charged amino acid
Two-dimensional gel electrophoresis

23. BIOINFORMATICS
The computer has become an important tool in genetic studies
Indeed, the marriage between genetics and biocomputing has yielded an important branch of science: bioinformatics
Computer analysis of genetic sequences usually relies on three basic components:
A computer
A computer program
Some type of data
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24. Computer Databases
The amount of genetic information that is generated by researchers has become enormous
Large numbers of computer data files are collected and stored in a single location, a database
The files in a database are typically annotated
They contain the genetic sequence and a concise description of it
In addition, they contain other features of significance
The scientific community has created several large databases containing data from thousands of labs
Refer to Table 21.3
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