Genomics, Bioinformatics, and Proteomics
Genomics
 We can divide the field of genomics into subfields
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Structural genomics
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Functional genomics
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Comparative genomics
Structural genomics
 This involves sequencing and the analysis of the sequences
 The development of genetic and physical maps starts the process
 We can use recombination frequencies to map various markers
 Genetic maps are limited by the resolution provided by recombination frequencies
 Physical maps are not
 Therefore, physical maps are inherently more accurate
 Whole-genome shotgun cloning and sequencing has become an extremely powerful
technique
 Sequencing entire genomes
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Individual chromosomes can be separated based on their size using flow
cytometry
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Enriching for a particular chromosome is followed by the production of
libraries consisting of fragments from that chromosome
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But you still have to put the pieces back together
 Another method is map-based
SNPs
 The technology has also allowed the identification of single-nucleotide
polymorphisms
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These are single-base-pair differences among members of a species
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Note: Different RFLP patterns are the result of particular SNPs (in
restriction enzyme sites)
 The particular set of SNPs and other genetic variants on a single chromosome is
called a haplotype
 If a SNP, or a series of SNPs, is located near a disease locus, it can be used to track the
disease allele
 Therefore, individuals with particular haplotypes will be more likely to carry a
particular disease allele
 This has led to the development of the human HapMap
CNVs
 Most genetic differences between individuals result from SNPs and copy number
variants (CNVs)
 These are the result of deletions and duplications
Bioinformatics
 Developed in response to the need for new computer algorithms to handle the vast
amounts of sequence data being generated
Functional genomics
The transcriptome consists of all of the RNA sequences produced via transcription
The proteome consists of all of the proteins encoded by the genome
Comparative genomics
 As more genomes are sequenced, we are getting a better picture of what makes each
species unique
Prokaryotes
 Results indicate that there has been substantial genetic exchange between both
closely and distantly related species - horizontal gene transfer
Eukaryotes
 Comparisons have revealed some very interesting trends and oddities
 Mice and humans have ~99% of their genes in common
 Fruit flies and humans have ~50%
 We share ~18% of our genes with plants!
 Comparative genomics has given us insight into the evolution and function of
multigene families
Metagenomics
 Metagenomics has provided new insights into our environment
Transcriptomics
 Transcriptome analysis can reveal differential gene expression
 Microarrays
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Can be used to analyze gene expression patterns
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We can look at gene expression patterns during specific periods of
development
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These gene chips have been very useful in determining how gene
expression changes under different conditions
Proteomics
 Analysis of the complete set of proteins found in a cell
 Because of epigenetics, this might prove much more informative than genomic
analysis
Systems biology
 In the future, it will be about the interactions - interactome
 In its rawest form, we can look at interactions between individual proteins
 Network maps group the interactions to match particular functions/conditions