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
