genomics - Genomics Chapter 10 Reconstructing the Genome...

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Genomics Chapter 10 Reconstructing the Genome Chapter 11 Comparison of Individual Genomes
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The genomes of living organisms vary enormously in size
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“Divide and conquer” strategy meets most challenges Chromosomes are broken into small overlapping pieces and cloned Ends of clones sequenced and reassembled into original chromosome strings Each piece is sequenced multiple times to reduce error rate 10-fold sequence coverage achieves a rate of error less than 1/10,000
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Fig. 10.2
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Techniques for mapping and cloning Cloning Library of DNA fragments 500 – 1,000,000 bp Insert into one of a variety of vectors Hybridization Location of a particular DNA sequence within the library of fragments PCR amplification Direct amplification of a particular region of DNA ranging from 1 bp to > 20kb DNA sequencing Automated DNA sequencer using Sanger method determines sequences 600-800 bp at a time (NOTE: New improved sequencing techniques are available now.) Computational tools Programs for identifying matches between a particular sequence and a large population of previously sequenced fragments Programs for identifying overlaps of DNA fragments Programs for estimating error rates Programs for identifying genes in chromosomal sequences
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Making a large scale linkage map Types of DNA polymorphisms used for large-scale mapping: Single nucleotide polymorphisms (SNPs) – 1/500 – 1/1000 bp across genome Simple sequence repeats (SSRs) – 1/20-1/40 kb across genome 2-5 nucleotides is repeated 4-50 or more times Most SNPs and SSRs have little or no effect on the organism Serve as DNA markers across the chromosomes Fig. 10.3
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Genome wide identification of genetic markers Initial genetic maps used SSRs which are highly polymorphic Identified by screening DNA libraries with SSR probes Amplified by PCR and length differences assayed SNPs – millions more recently identified by comparison of orthologous regions of cDNA clones from different individuals
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Homologous – genes with enough sequence similarity to be related somewhere in evolutionary history Orthologous – genes in two different species that arose from the same gene in the two species’ common ancestor Paralogous – arise by duplication within same species Orthologous genes are always homologous, but homologous genes are not always orthologous SOME VOCABULARY
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Physical maps Overlapping DNA fragments ordered and oriented that span each of the chromosomes Based on direct analysis of DNA rather than
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This note was uploaded on 12/17/2009 for the course BIO 2354 taught by Professor Brockett during the Spring '08 term at Georgia Tech.

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genomics - Genomics Chapter 10 Reconstructing the Genome...

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