Lec1-SequencingAndAssembly2007

Lec1-SequencingAndAssembly2007 - Announcements • Lab...

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Unformatted text preview: Announcements • Lab tomorrow morning at 9:30 • For Tuesday: read wooly mammoth genome paper and bring a printed version of three questions/topics for discussion • Discussion leader selection Sequencing and Assembly The Relic, 1997 GEN875, Genomics and Proteomics, Fall 2007 Questions • What do we sequence? • Why do we sequence it? – How do we sequence it? Explosive Growth in Sequencing 8/22/2005 Press Release: INSD (GenBank, EMBL, DDBJ) reaches 100 Gigabase milestone What do we sequence? • Genomes (de novo, resequencing) • Metagenomes or complex samples • Transcripts NCBI Genomes http://www.ncbi.nlm.nih.gov/Genomes/ Eukaryotic Genomes: Complete 25, 22, 20 Assembly 162, 109, 72 In progress 235, 299, 166 Prokaryotic Genomes: Complete 567, 371, 254 In progress 841, 615, 433 Comparison of data from 9/5/07, 9/4/06 and 8/31/05 Genome Projects 100 200 300 400 500 600 700 800 900 Year Number of Genomes Euk-Done Euk-In Progess Prok-Done Prok-In Progress Why do we sequence genomes? Why do we sequence genomes? • To catalog all the genes present in one organism. • To compare the gene content of one organism to another organism. • To study features other than genes. • To study genome evolution. • To study organismal evolution. • As a foundation for future experimentation. Complete vs. Draft genomes? • To catalog all the genes present in one organism. • To compare the gene content of one organism to another organism. • To study features other than genes. • To study genome evolution. • To study organismal evolution. • As a foundation for future experimentation. DNA sample Sequencing Center JCVI/TIGR Broad Institute JGI Joint Genome Institute Washington University Baylor College of Medicine Sanger Centre Etc. GATCGATCGATC… + Annotation Strategies • Clone and sequence (select or random) clones using Sanger sequencing • Massively parallel pyrosequencing (454) • “proprietary Clonal Single Molecule Array technology and novel reversible terminator-based sequencing” (Solexa) Method Comparison WGS 454 Solexa Cloning Yes No No Chemistry Sanger pyrosequencing reversible terminators Cost $$$$ to $$$$$$$ $$ $$ Accuracy Consensus 99.99% Single read > 99.5%; Consensus > 99.99% ? Assembly Best Better Bad Gap Closure and Finishing Tough Tougher Possible? Bacterial Culture Isolate DNA Physical fragmentation Size selection Ligate randomly into vectors Transformation Plate on agar Pick and grow individual colonies Isolate cloned constructs Cycle Sequencing High-throughput Steps Library construction and sequencing Bacterial Culture Isolate DNA Physical fragmentation Size selection Ligate randomly into vectors Transformation Plate on agar Pick and grow individual colonies Isolate cloned constructs Cycle Sequencing High-throughput Steps Library construction and sequencing What if you can’t grow it?...
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This note was uploaded on 08/08/2008 for the course GEN 875 taught by Professor Glasner during the Fall '07 term at Wisconsin.

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Lec1-SequencingAndAssembly2007 - Announcements • Lab...

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