36_Lieb_Genomics_I

36_Lieb_Genomics_I - Genomics I: Wholegenome Sequencing and...

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Genomics I: Whole-genome  Sequencing and  Comparison J. Lieb
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Review of Last Lecture: Reverse Genetics Gene   Phenotype or Molecular Analysis First   Mutations Second Example Uses:   Understand the function of a gene homolog characterized in another  organism   Understand the function of individual amino acids or protein domains.   Create “conditional alleles” of a gene.
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What Is Genomics? Genomics is the study of how entire genomes function  as a unit Ranging from how they operate at the molecular  level (transcription, replication, recombination,  etc.)  to how whole genomes evolve over time. 
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Bioinformatics:  Analysis of the information content of  genomes Comparative Genomics:   Compares genome sequences with each other to infer  evolutionary relationships and mechanisms of evolution Functional Genomics:  Perform experiments in the lab that probe how  genomes function as a whole.  DNA microarrays, RNAi libraries, deletion collections,  and whole-genome systems for detecting protein-DNA  interactions.  Three broad areas of genomics
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Why Sequence Whole Genomes?   To speed characterization of genes  mapped by linkage   To obtain a "parts list" for what  makes up an organism.  All of the  instructions are there, and the book is in  front of us. Now, we just need to figure  out what it all means.   To discover what sets of genes  make organisms (and each of us)  similar to and different from one  another.    To understand our evolutionary  heritage. Our genomes are a reflection  of our recent and ancient origins. 
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In the 1980's, all of the tools were in place for  genome sequencing to begin   Vectors for making genomic libraries   PCR for amplifying genes   DNA sequencing machines How Are Genomes Sequenced? But sequencing was too slow and too  expensive to go for whole genomes
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A strategy called Shotgun sequencing , coupled with advances in  sequencing technology, robotics, and computers, made  "Genomics" possible 1. Blow genome to bits 2. Sequence the little bits 3. Put all the little bits back  together in the right order based  on their sequence 4. Assemble  longer and longer  pieces until the genome is  complete. 
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Whole-Genome Shotgun Sequencing * computer-intensive:   Celera made 500,000,000,000,000,000 base-base  comparisons; 20,000 hours CPU time * must sequence several-fold:   Celera did 4.6X sequencing: 26.4 million sequences of 550 bp each = 14.5 billion bp (3.2 billion in human  genome) * some regions might not get sequenced, leading to gaps in assembly * repetitive sequences can cause errors in assembly * SNPs and other polymorphisms can complicate assembly Close-up of an individual sequence assembly
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There are always some gaps after shotgun  sequencing
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36_Lieb_Genomics_I - Genomics I: Wholegenome Sequencing and...

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