Need to Add to part 2 or 3 A. Chip-seq B. Deep sequencing for expression profiling C. Illumina? movie Genomics Summary A. Microarrays: expression profiling and other uses B. Global Gene Knockouts C. Global protein localization in yeast D. Global complex identification in yeast E. Global two-hybrid analysis in yeast and other organisms F. RNAi G. Transgenics, gene “knock-outs” (genetics not genomics) H. Human Genome Project, Next Generation Sequencing, and Comparative Genomics Yeast “Knockout” Library Delete YFG Delete all genes (individually) Disruption of “All” Yeast Genes • Approx 6000 genes • Make 6000 sets of disruption primers ...
• Metagenomics • Whole-genome shotgun sequencing • Environmental metagenomics • Human microbiome –Precision medicine • Conclusion Metagenomics • Environmental genomics. • DNA analysis without lab-based cultivation. • Better understanding of community-based microbial biology, ecology, and evolution. Whole-genome shotgun sequencing Environmental Genome Shotgun Sequencing of the Sargasso Sea. Venter et al. (2004) • 1.045 billion base pairs of nonredundant sequence. – Gene content, diversity, and relative abundance of the organisms. – At least 1.800 genomic species based on sequence relatedness. – At least 148 previously unknown bacterial phylotypes. – Over 1.2 million previously unknown genes . • Quantitative ...
Assembling a gene sequence Align sequencing reads to generate a series of overlapping sequences that cover the gene. Sequencing both strands is more accurate. 08/28/2022 Hardison, R (1983) J. Biol. Chem. 258:8739-8744 2 Align multiple sequencing reads Sequencher Gene Codes Corp. Stephan Schuster 08/28/2022 3 Contig assembly Assembly of libraries with 3 different insert sizes gap plasmid library (4-5 kb) plasmid library (1-3 kb) BAC library (130-2000 kb) 08/28/2022 Stephan Schuster 4 Dealing with Gb, not Mb • Sizes of genomes vary over orders of magnitude – Bacterial: about 1 to 6 Mb – Yeast (Saccharomyces cerevisiae): 12 Mb &ndash ...
DNA fragment sequencing In order to establish exactly what changes have occurred in the gene under study, it will be necessary determine the DNA sequence of that gene. This is now a routine procedure in molecular biology laboratories, extending not just to individual genes or fragments but to the complete sequence of the DNA (the genome) of the organism. The two main in vitro DNA sequencing methods were published in 1977, a few months apart, by Maxam and Gilbert and by Sanger et al. and will revolutionize in the same way as for PCR molecular biology and its applications in ...
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