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BCB 444/544. Lecture 34 Comparative Genomics #34_Nov12. Required Reading ( before lecture). 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

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BCB 444/544


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    1. BCB 444/544 Lecture 34 Comparative Genomics #34_Nov12 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    2. Required Reading (before lecture) 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 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    3. 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) BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    4. 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 Seminar2:10 in 102 SciI • Karin DormanISU • Modeling HIV-host interactions BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    5. 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 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    6. 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, NHGRITGA2005Lecture13.pdf 4- Comparative Genomics Comparative Sequence Analysis Elliott Margulies, NHGRI CTGA2005Lecture8.pdf BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    7. 1- Genomic sequencingMany thanks to:Eric Green, NHGRI for the following slides extracted from his lecture on:Mapping and SequencingCTGA2005Lecture1.pdf BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    8. Sequencing Method #1: Gilbert-Maxim "Chemical Degradation" E Green 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    9. Sequencing Method #2: Sanger "Di-deoxy Chain Termination" E Green 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    10. 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) E Green 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    11. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Pyrosequencing.htmlhttp://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Pyrosequencing.html Recent technologies? Pyro-Sequencing BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    12. Massively Parallel Sequencing: 454 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    13. Massively Parallel Sequencing: 454 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    14. But years BEFORE these Massively Parallel Technologies, Human Genome Sequence was completed much faster than expected! E Green 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    15. 1st Draft Human Genome: ”Complete" in 2001 E Green 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    16. "Finishing" the Human Genome - continues… E Green 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    17. After "Complete" Human Genome Sequence What next? E Green 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    18. Eric Green's Genomic Sequencing Challenges (2005 List) E Green 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    19. ENCODE Project E Green 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    20. ENCODE - Web Sites E Green 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    21. ENCODE - Results? June 2007 http://www.nature.com/nature/journal/v447/n7146/full/nature05874.html BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    22. Comparative Genomics: now with complete genomic sequences E Green 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    23. Comparing Genomes: Functional Elements BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics E Green 2005

    24. Was It Really Worth all that $$? & Who Owns it Now??? http://www.i-sis.org.uk/humangenome.php BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    25. Speaking of Craig Venter - What is the “Cutting-Edge” in Sequencing Technologies? http://www.jcvi.org/ BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    26. MetaGenomic Sequencing: Entire Marine Populations!! http://www.jcvi.org/press/news/news_2007_03_13.php BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    27. 2- Human Genome ProjectMany thanks to:Jonathan Pevsner Kennedy Krieger Institutefor the following slides extracted from his lecture on:The Human Genome2005-10-19_ch17.pdf BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    28. Human Genome Sequence - Where is it? J Pevsner 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    29. Human Genome Project: What have we learned? 20,000 - 25,000 2004 J Pevsner 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    30. Our genome size = Pufferfish or Arabidopsis J Pevsner 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    31. Many human genes (~50%) are subject to alternative splicing J Pevsner 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    32. Lots of lateral transfer from bacteria??? J Pevsner 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    33. Lots of transposons & segmental duplications J Pevsner 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    34. 3% of human genome = Alu repeats (short repetitive elements from ancient transposons) J Pevsner 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    35. And what women have known all along: J Pevsner 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    36. Lots of SNPs: single nucleotide polymorphisms J Pevsner 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    37. 3- SNPsMany thanks to:Jim Mullikin, NHGRI for the following slides extracted from his lecture on:Studying Genetic Variation II: Computational TechniquesCTGA2005Lecture13.pdf BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    38. SNPs: Single Nucleotide Polymorphisms J Mullikin 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    39. SNPs: Single Nucleotide Polymorphisms J Mullikin 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    40. SNP Discovery Methods J Mullikin 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    41. SNPs - from EST Mining J Mullikin 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    42. SNPs: from Clone Overlap J Mullikin 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    43. The SNP Consortium (TSC) J Mullikin 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    44. Haplotype Map (HapMap) Project J Mullikin 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    45. SNPs: from Targeted Resequencing J Mullikin 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    46. Using PolyPhred to Visualize SNPs J Mullikin 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    47. SNPs: from Sequencing Chips J Mullikin 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    48. "SNP Chips": an example J Mullikin 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    49. SNPs: How are they distributed? J Mullikin 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics

    50. SNPs: How are they distributed? J Mullikin 2005 BCB 444/544 F07 ISU Dobbs #34 - Comparative Genomics