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Introduction to Bioinformatics

Introduction to Bioinformatics. Lecturer: Prof. Yael Mandel-Gutfreund Teaching Assistance: Rachelly Normand Edward Vitkin. Course web site : http://webcourse.cs.technion.ac.il/236523. What is Bioinformatics?. Course Objectives. To introduce the bioinfomatics discipline

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Introduction to Bioinformatics

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  1. Introduction to Bioinformatics Lecturer: Prof. Yael Mandel-Gutfreund Teaching Assistance: Rachelly Normand Edward Vitkin Course web site : http://webcourse.cs.technion.ac.il/236523

  2. What is Bioinformatics?

  3. Course Objectives • To introduce the bioinfomatics discipline • To make the students familiar with the major biological questions which can be addressed by bioinformatics tools • To introduce the major tools used for sequence and structure analysis and explainin general how they work (limitation etc..)

  4. Course Structure and Requirements • Class Structure • 2 hours Lecture • 1 hour tutorial 2. Home work • Homework assignments will be given every second week • The homework will be done in pairs. • 5/5 homework assignments will be submitted 2. A final project will be conducted in pairs * Project will be presented as a poster –poster day 19.3

  5. Grading • 20 % Homework assignments • 80 % final project (10% proposal, 20% supervisor evaluation 70% poster presentation)

  6. Literature list • Mount, D.W. Bioinformatics: Sequence and Genome Analysis. 2nd ed.,Cold Spring Harbor Laboratory Press, 2004. Advanced Reading Jones N.C & Pevzner P.A. An introduction to Bioinformatics algorithms MITPress, 2004

  7. What is Bioinformatics?

  8. What is Bioinformatics? “The field of science in which biology, computer science, and information technology merge to form a single discipline” Ultimate goal: to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned.

  9. 21ST centaury Genome Transcriptome Proteome Central Paradigm in Molecular Biology Gene (DNA) mRNA Protein

  10. From DNA to Genome Watson and Crick DNA model 1955 1960 1965 1970 1975 1980 1985

  11. 1990 First genome Hemophilus Influenzae 1995 Yeast genome First human genome draft 2000

  12. Complete Genomes Total 1379 294 Eukaryotes 133 39 Bacteria 1152 235 Archaea 94 23 20102005 Total complete genomes 10.10.13 = 7381

  13. 1,000 Genomes Project: Expanding the Map of Human Genetics Researchers hope the effort will speed up the discovery of many diseases's genetic roots

  14. 25000 genomes… What’s Next ? The “post-genomics” era Systems Biology Functional genomics Annotation Comparative genomics Main Goal: To understand the living cell

  15. And beyond…Personalized medicine

  16. From ….25000 genomes To…Understanding living cells

  17. Annotation CCTGACAAATTCGACGTGCGGCATTGCATGCAGACGTGCATG CGTGCAAATAATCAATGTGGACTTTTCTGCGATTATGGAAGAA CTTTGTTACGCGTTTTTGTCATGGCTTTGGTCCCGCTTTGTTC AGAATGCTTTTAATAAGCGGGGTTACCGGTTTGGTTAGCGAGA AGAGCCAGTAAAAGACGCAGTGACGGAGATGTCTGATG CAA TAT GGA CAA TTG GTT TCT TCT CTG AAT ...... .............. TGAAAAACGTA

  18. Identify the genes within a given sequence of DNA Identify the sites Which regulate the gene Annotation Predict the function What do they do???

  19. How do we identify a gene in a genome? A gene is characterized by several features (promoter, ORF…) some are easier and some harder to detect…

  20. Using Bioinformatics approaches for Gene hunting Relative easy in simple organisms (e.g. bacteria) VERY HARD for higher organism (e.g. humans)

  21. Comparative genomics

  22. Perhaps not surprising!!! How humans are chimps? Comparison between the full drafts of the human and chimp genomes revealed that they differ only by 1.23% How can we be so similar--and yet so different?

  23. Where are we different ?? Where are we similar ??? VERY SIMAILAR Conserved between many organisms VERY DIFFERENT

  24. Sometime minor changes in critical genes can make a big difference Human ATAGCGGGGGGATGCGGGCCCTATACCC Chimp ATAGGGGGGATGCGGGCCCTATACCC Mouse ATAGCGGGATGCGGCGCTATACCA Human ATAGCGGGGGGATGCGGGCCCTATACCC Chimp ATAGGGG--GGATGCGGGCCCTATACCC Mouse ATAGCG---GGATGCGGCGC-TATACC-A

  25. Single change in a genes among humans can be responsible for sever diseases Sickle Cell Anemia Due to 1 swapping of an A for a T Image source: http://www.cc.nih.gov/ccc/ccnews/nov99/

  26. Healthy Individual >gi|28302128|ref|NM_000518.4| Homo sapiens hemoglobin, beta (HBB), mRNA ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGA GGAGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGC AGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATG CTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGC TCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGAT CCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCA CCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCA CTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACT GGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC >gi|4504349|ref|NP_000509.1| beta globin [Homo sapiens] MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN ALAHKYH

  27. Diseased Individual >gi|28302128|ref|NM_000518.4| Homo sapiens hemoglobin, beta (HBB), mRNA ACATTTGCTTCTGACACAACTGTGTTCACTAGCAACCTCAAACAGACACCATGGTGCATCTGACTCCTGA GGTGAAGTCTGCCGTTACTGCCCTGTGGGGCAAGGTGAACGTGGATGAAGTTGGTGGTGAGGCCCTGGGC AGGCTGCTGGTGGTCTACCCTTGGACCCAGAGGTTCTTTGAGTCCTTTGGGGATCTGTCCACTCCTGATG CTGTTATGGGCAACCCTAAGGTGAAGGCTCATGGCAAGAAAGTGCTCGGTGCCTTTAGTGATGGCCTGGC TCACCTGGACAACCTCAAGGGCACCTTTGCCACACTGAGTGAGCTGCACTGTGACAAGCTGCACGTGGAT CCTGAGAACTTCAGGCTCCTGGGCAACGTGCTGGTCTGTGTGCTGGCCCATCACTTTGGCAAAGAATTCA CCCCACCAGTGCAGGCTGCCTATCAGAAAGTGGTGGCTGGTGTGGCTAATGCCCTGGCCCACAAGTATCA CTAAGCTCGCTTTCTTGCTGTCCAATTTCTATTAAAGGTTCCTTTGTTCCCTAAGTCCAACTACTAAACT GGGGGATATTATGAAGGGCCTTGAGCATCTGGATTCTGCCTAATAAAAAACATTTATTTTCATTGC >gi|4504349|ref|NP_000509.1| beta globin [Homo sapiens] MVHLTPVEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN ALAHKYH

  28. Functional genomics

  29. TO BE IS NOT ENOUGH In any time point a gene can be functional or not

  30. The difference in the brain size between Human and apes is mainly related to the different levels of the genes expression and not their content

  31. Systems Biology

  32. Biological networks Jeong et al. Nature411, 41 - 42 (2001)

  33. What can we learn from Biological Networks What can we learn about this protein • Is the protein essential for the organism ? • Is it a good drug targets?

  34. How can bioinformatics contribute to Medicine? http://www.tedmed.com/talks/show?id=17961

  35. What of all this will we learn in the course? The course will concentrate on the bioinformatics tools and databases which are used to : - Annotate genes, - Compare genes and genomes - Infer the function of the genes and proteins - Analyze the interactions between genes and proteins ETC….

  36. Main Topics 1. Introduction to bioinformatics 2. Pairwise alignment 3. Database search 4. Protein alignments 5. MSA and phylogenetic analysis 6. Sequencing 7. Motif search-function prediction 8. Gene expression 9. Structural bioinformatics (proteins and RNA) 10. Biological networks

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