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791_cb_lecture1

791_cb_lecture1 - 7.91 7.36 BE.490 Lecture#1 Feb 24 2004...

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7.91 / 7.36 / BE.490 Lecture #1 Feb. 24, 2004 Genome Sequencing & DNA Sequence Analysis Chris Burge
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What is a Genome? A genome is NOT a bag of proteins
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What’s in the Human Genome?
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Outline of Unit II: DNA/RNA Sequence Analysis Reading* 2/24 2/26 3/2 M Ch. 4 3/4 M Ch. 4 3/9 DNA Sequence Evolution 3/11 RNA Structure Prediction & Applications M Ch. 5 3/16 Literature Discussion TBA Genome Sequencing & DNA Sequence Analysis M Ch. 3 DNA Sequence Comparison & Alignment M Ch. 7 DNA Motif Modeling & Discovery Markov and Hidden Markov Models for DNA M Ch. 6 * M = Mount, “Bioinformatics: Sequence and Genome Analysis”
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Feedback to Instructor Examples from past years: • Comic font looks stupid • Burge uses too much genomics jargon • Better synergy between Yaffe/Burge sections • Asks questions to the class, student answers, but I didn’t hear/understand the answer…
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DNA vs Protein Sequence Analysis Protein Sequence Analysis DNA Sequence Analysis - emphasis on chemistry - emphasis on regulation - protein structure - RNA structure - selection is everywhere - signal vs noise ( statistics ) - multiple alignment - motif finding - comparative proteomics - comparative genomics - data: O(10^8) aa - data: O(10^10) nt Read your probability/statistics primer!
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Genome Sequencing & DNA Sequence Analysis The Language of Genomics Shotgun Sequencing DNA Sequence Alignment I Comparative Genomics Examples - Progress: genomes, transcriptomes, etc. - How to choose a mismatch penalty - PipMaker, Phylogenetic Shadowing
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Recent Media Attention
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Genomespeak Bork, Peer, and Richard Copley. " Genome Speak." Nature 409 (15 February 2001): 815. Learn to speak genomic
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In the following article, note the use of the following genomic terms: euchromatic, whole-genome shotgun sequencing, sequence reads, 5.11-fold coverage, plasmid clones, whole-genome assembly, regional chromosome assembly.
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