Chapter_12_-_Genomic_Analysis_v2

Chapter_12_-_Genomic_Analysis_v2 - Genomic Analysis...

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Genomic Analysis
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12.1 Genome Sequencing 12.1.1 Overview 470 completed genome sequences by 2007 many first ones sequences were small genomes (bacteria / archaeal / viruses) serve as endosymbionts and use host cell to carry out necessary functions Once contigs are assembled and >80-90% most of the sequence is known (there may be many gaps or uncertainties in the sequence it is known as a draft sequence A finished sequence will contain no obvious gaps or uncertainties in the sequence The final sequence has to be annotated where protein-coding sequence are identified and predictions are made as to the nature of the products
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12.1 Genome Sequencing  12.1.3 Strategies Race to sequence the human genome 2001 Governmental agencies (eg. NIH) broke down each chromosome created an ordered library of inserts different laboratories were given identified regions to sequence Placement of the sequenced regions were known before assembly of the genome Celeron (private company) used a shotgun sequencing approach Random fragments were sequenced until whole genome was covered Lots of redundant, overlapping sequences Computing power used to assemble overlapping fragments Paradoxically, Celeron completed the human genome sequencing first
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Humans, Homo sapiens; see Human genome project Neanderthal, "Homo neanderthalensis" (partial) Haemophilus influenzae, a bacterium (the first free-living organism to have its genome fully sequenced) Common House Mouse, Mus musculus Brown Rat, Rattus norvegicus Common Chimpanzee Pan troglodytes; see Chimpanzee Genome Project Rhesus Macaque, Macaca mulatta Domestic Chicken, Gallus gallus Tammar Wallaby, Macropus eugenii Domestic Cat, Felis silvestris Domestic Dog, Canis lupus familiaris Common fruit fly, Drosophila melanogaster Baker's yeast, Saccharomyces cerevisiae Red bread mold, Neurospora crassa Thale Cress, Arabidopsis thaliana Rice, Oryza sativa Common Wheat, Triticum aestivum Maize, Zea mays Poplar, Populus trichocarpa Escherichia coli, a coliform bacterium SARS virus Purple-spined sea urchin, Arbacia punctulata Caenorhabditis elegans, a nematode worm Zebra Danio, Brachydanio rerio African clawed frog, Xenopus laevis Oryzias latipes, a medakafish Tiger blowfish, Takifugu rubipres Tomato Solanum lycopersicum Potato Solanum tuberosum Western Honey bee, Apis mellifera Grapevine, Vitis vinifera L. Spanish flu 12.1 Genome Sequencing - Examples of genome  projects
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12.1 Genome Sequencing  12.1.5 Repetitive elements and gaps Contig assembly is complicated by: Repetitive DNA (at least 50% of the human genome) Segmental duplications of blocks of 100+ kb to a different part of the genome Mobile elements such as transposons and insertion sequences Tandem repeats of short sequences
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This note was uploaded on 07/10/2010 for the course BIOL 208 taught by Professor Chuong during the Spring '09 term at Waterloo.

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Chapter_12_-_Genomic_Analysis_v2 - Genomic Analysis...

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