麻省理工大学：《Foundations of Biology》课程教学资源（英文版）Lecture 1 Genome Sequencing

791/7.36/BE490 Lecture #f1 Feb.24,2004 Genome Sequencing 8 DNA Sequence Analysis Chris burge

7.91 / 7.36 / BE.490 Lecture #1 Feb. 24, 2004 Genome Sequencing & DNA Sequence Analysis Chris Burge

What is a genome? 123456789101112 13141516171819202122XY A genome is NoT a bag of proteins

What is a Genome? A genome is NOT a bag of proteins

What's in the human genome?

What’s in the Human Genome?

Outline of unit ll DNARNA Sequence Analysis Reading 2/24 Genome Sequencing DNA Sequence Analysis MCh. 3 2/26 DNA Sequence Comparison Alignment MCh. 7 3/2 DNA Motif Modeling Discovery M Ch 4 3/4 Markov and Hidden markov Models for dna MCh. 4 3/9 DNA Sequence Evolution MCh. 6 3/11 RNA Structure Prediction Applications MCh. 5 3/16 Literature Discussion TBA M=Mount, Bioinformatics: Sequence and Genome Analysis

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

Feedback to Instructor EXamples from past years Comic font looks stupid Burge uses too much genomics jargon Better synergy between yaffeBurge sections Asks questions to the class, student answers but i didn 't hear/understand the answer

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…

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(10410)nt Read your probability/statistics primer

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!

Genome Sequencing DNA Sequence Analysis The Language of genomics Shotgun Sequencing Progress: genomes, transcriptomes, etc DNA Sequence Alignment I How to choose a mismatch penalty Comparative Genomics EXamples PipMaker, Phylogenetic Shadowing

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

Recent media attention The Human Genome (and cloning) The rest of Biology

Recent Media Attention

Genomespeak Bork, Peer, and Richard Copley. "Genome Speak Nature 409(15 February 2001 ): 815 Learn to speak genomic

Genomespeak Bork, Peer, and Richard Copley. " Genome Speak." Nature 409 (15 February 2001): 815. Learn to speak genomic

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 Venter, JC, MD Adams, EW Myers, PWLi, Rj Mural, GG Sutton HO Smith ,...The Sequence of The Human Genome. Science 291, no 5507 (16 February 2001 ): 1304-51

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. Venter, JC, MD Adams, EW Myers, PW Li, RJ Mural, GG Sutton, HO Smith, … "The Sequence of The Human Genome." Science 291, no. 5507 (16 February 2001): 1304-51