Comparative Genomics: Lecture 34 - Methods and Technologies - Prof. Drena Leigh Dobbs, Lab Reports of Bioinformatics

Download Comparative Genomics: Lecture 34 - Methods and Technologies - Prof. Drena Leigh Dobbs and more Lab Reports Bioinformatics in PDF only on Docsity! #34 - Comparative Genomics 11/12/07 BCB 444/544 Fall 07 Dobbs 1 1BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 BCB 444/544 Lecture 34 Comparative Genomics #34_Nov12 2BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 Mon Nov 12 - Lecture 34 Comparative Genomics •Chp 17 Wed Nov 14 - Lecture 35 Functional Genomics • Chp 18 Thurs Nov 15 - Lab 11 Microarray Analysis Fri Nov 16 - Lecture 36 Proteomics • Chp 19 Required Reading (before lecture) 3BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 Assignments & Announcements Fri Nov 9 - HW#6 (was not posted this weekend!) HW#6 - More fun with Machine Learning!! Nope: Instead: Fun with Gene Annotation!! Due: whenever… (sometime before Mon Nov 26) 4BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 Seminars this Week BCB List of URLs for Seminars related to Bioinformatics: http://www.bcb.iastate.edu/seminars/index.html • Nov 12 Mon - Math Seminar 4:10 in Carver • Trachette Jackson Univ of Michigan •Mathematical Modeling of Angiogenesis in Cancer • Nov 16 Fri - BCB Faculty Seminar 2:10 in 102 SciI • Karin Dorman ISU •Modeling HIV-host interactions 5BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 Chp 17 – Comparative Genomics SECTION V GENOMICS & PROTEOMICS Xiong: Chp 17 Genome Mapping, Assembly & Comparison • Genome Mapping • Genome Sequencing • Genome Sequence Assembly • Genome Annotation • Comparative Genomics 6BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 Genomics - for excellent overview lectures, see these posted by NHGRI & Pevsner: 1- Genomic sequencing Mapping and Sequencing CTGA2005Lecture1.pdf Eric Green, NHGRI 2- Human genome project The Human Genome 2005-10-19_ch17.pdf Jonathan Pevsner, Kennedy Krieger Institute 3- SNPs Studying Genetic Variation II: Computational Techniques Jim Mullikin, NHGRI TGA2005Lecture13.pdf 4- Comparative Genomics Comparative Sequence Analysis Elliott Margulies, NHGRI CTGA2005Lecture8.pdf #34 - Comparative Genomics 11/12/07 BCB 444/544 Fall 07 Dobbs 2 7BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 1- Genomic sequencing Many thanks to: Eric Green, NHGRI for the following slides extracted from his lecture on: Mapping and Sequencing CTGA2005Lecture1.pdf 8BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07E Green 2005 Sequencing Method #1: Gilbert-Maxim "Chemical Degradation" 9BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07E Green 2005 Sequencing Method #2: Sanger "Di-deoxy Chain Termination" 10BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07E Green 2005 Automated Sequencing for Genome Projects: Sanger method - with improvements Another “recent” improvement: rapid & high resolution separation of fragments in capillaries instead of gels (E Yeung,Ames Lab, ISU) 11BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 Recent technologies? Pyro-Sequencing http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Pyrosequencing.html 12BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 Massively Parallel Sequencing: 454 #34 - Comparative Genomics 11/12/07 BCB 444/544 Fall 07 Dobbs 5 25BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 Speaking of Craig Venter - What is the “Cutting-Edge” in Sequencing Technologies? http://www.jcvi.org/ 26BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 MetaGenomic Sequencing: Entire Marine Populations!! http://www.jcvi.org/press/news/news_2007_03_13.php 27BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 2- Human Genome Project Many thanks to: Jonathan Pevsner Kennedy Krieger Institute for the following slides extracted from his lecture on: The Human Genome 2005-10-19_ch17.pdf 28BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Pevsner 2005 Human Genome Sequence - Where is it? 29BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Pevsner 2005 Human Genome Project: What have we learned? 20,000 - 25,000 2004 30BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Pevsner 2005 Our genome size = Pufferfish or Arabidopsis #34 - Comparative Genomics 11/12/07 BCB 444/544 Fall 07 Dobbs 6 31BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Pevsner 2005 Many human genes (~50%) are subject to alternative splicing 32BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Pevsner 2005 Lots of lateral transfer from bacteria??? 33BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Pevsner 2005 Lots of transposons & segmental duplications 34BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Pevsner 2005 3% of human genome = Alu repeats (short repetitive elements from ancient transposons) 35BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Pevsner 2005 And what women have known all along: 36BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Pevsner 2005 Lots of SNPs: single nucleotide polymorphisms #34 - Comparative Genomics 11/12/07 BCB 444/544 Fall 07 Dobbs 7 37BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 3- SNPs Many thanks to: Jim Mullikin, NHGRI for the following slides extracted from his lecture on: Studying Genetic Variation II: Computational Techniques CTGA2005Lecture13.pdf 38BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Mullikin 2005 SNPs: Single Nucleotide Polymorphisms 39BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Mullikin 2005 SNPs: Single Nucleotide Polymorphisms 40BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Mullikin 2005 SNP Discovery Methods 41BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Mullikin 2005 SNPs - from EST Mining 42BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Mullikin 2005 SNPs: from Clone Overlap #34 - Comparative Genomics 11/12/07 BCB 444/544 Fall 07 Dobbs 10 55BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 Hapmap Project http://www.hapmap.org/ 56BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Mullikin 2005 HapMap Project Goals 57BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 HapMap Results: http://www.hapmap.org/ 58BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07J Mullikin 2005 Significance of SNP Analyses 59BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 4- Comparative Genomics Many thanks to: Elliott Margulies, NHGRI for the following slides extracted from his lecture on: Comparative Sequence Analysis CTGA2005Lecture8.pdf 60BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07E Margulies 2005 #34 - Comparative Genomics 11/12/07 BCB 444/544 Fall 07 Dobbs 11 61BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07E Margulies 2005 Comparative Genomics 62BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07E Margulies 2005 Comparative Genomics Provides Important Clues re: Biological Function of Genes 63BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07E Margulies 2005 Different Terms are used to Describe Different types of Conserved Sequences 64BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07E Margulies 2005 Sequence Comparisons Whole Genome Alignments! 65BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07E Margulies 2005 Two Major Visualization Tools: 66BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 E Margulies 2005 zPicture: Best of Both Tools: #34 - Comparative Genomics 11/12/07 BCB 444/544 Fall 07 Dobbs 12 67BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07E Margulies 2005 Comparing Multiple Species with zPicture 68BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07E Margulies 2005 What Have We Learned from Comparative Genomics? An early example: 69BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 What Have We Learned from Comparative Genomics? A more recent example: Re: Pollard KS, …Haussler D. (2006) An RNA gene expressed during cortical development evolved rapidly in humans. Nature 443: 167-172. PDF 70BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 ISU Resources & Experts (a few of them) Genomic sequencing & comparative genomics Facilities: ISU Biotech DNA Facility PSI Carver Co-Lab Experiments: Microbial: Minion, others Plant: Schnable, Wise, Bogdonave, many others Animal: Rothschild, Tuggle, Reecy, Lamont, many others Assembly & Analysis: Huang, Chou, Brendel, Proulx, Gu 71BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics 11/12/07 Optional Reading Human HapMap The Project: (Nature 437, Oct 27, 2005) • Commentary (437:1233) http://www.nature.com/nature/journal/v437/n7063/full/4371233a.html • News & Views (437: 1241) http://www.nature.com/nature/journal/v437/n7063/full/4371241a.html • Article (437:1299) A haplotype map of the human genome The International HapMap Consortium The Results: