MMG433 ReviewStudyGuide

MMG433 ReviewStudyGuide - MMG 433: Review/Study Guide...

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MMG 433: Review/Study Guide Lecture 1: Two approaches to Genomics: Philosophical – New way to approach biological problems Practical – High throughput methods for analyzing biological systems DNA Sequencing: 1392 complete bacterial genomes currently in Entrez Genome database; >3500 draft genomes in database, prob. 50K done but not deposited. New sequencing methods on the horizon: Goal – 1000 human genome, $1 bacterial genome, Genetic mapping in bacteria – obsolete, PacBio=10Gb/hr sequencing technology. Functional Genomics: DNA microarray Proteomics: 2-D gel electrophoresis Structural Genomics: 3-D structure High-throughput genetics : Determine the function of every gene in a genome. Determine the genes essential for life; Minimal genome concept, Mycoplasma – 500 genes, 256 genes estimate for life – can we build a bacterium? The Informatics Problem: There are approximately 106,633,156,756 bases in 108,431,692 sequence records in the traditional GenBank divisions and 148,165,117,763 bases in 48,443,067 sequence records in the WGS division as of August 2009 Over 50 Million PubMed searches are preformed each month Microarrays, proteomics, networks How is this much data handled? Lab 1: NCBI, PubMed tutorials, familiarize with Macbooks. Lecture 2: Microbial Genomes: Microbial Genome; -old view ( E. coli ): Single chromosome, Circular, Replication initiates from a single fixed origin, little or no horizontal gene transfer. -new view: Bacteria can contain more than one chromosome, Bacterial chromosomes can be linear, Horizontal gene transfer is common, expect the unexpected. Features: -4 bases: AGCT
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Establishing gene function – bioinformatics can only get you so far. Book – claims that over 75% of genes can be assigned function; many annotations suggest biochemical role, not biological function, many annotations need to be verified experimentally, some annotations are wrong. Benefits to sequencing microbial genomes: -Develop technology for human genome project -Examine the genomes of wide range of microbes: novel drug/vaccine targets, Identify new agricultural and industrial important enzymes, comparative genomics/evolution, sequence microbes that have no genetics, sequence microbes we can’t culture – metagenomics -Because we can -Goal is to be able to sequence a human genome for $1000: (Human genome project took 13
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MMG433 ReviewStudyGuide - MMG 433: Review/Study Guide...

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