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Introduction to Bioinformatics Introduction to Bioinformatics Dr. rer. nat. Jing Gong Cancer Research center Medicine School of Shandong University 2011.9.14 1 Introduction to Bioinformatics Chapter 1 Introduction 2 Introduction to Bioinformatics About me • Dr. rer. nat. Jing Gong • Bachelor Degree in Marine Biology at the China Ocean University (former Qingdao Ocean University) • Bachelor, Master & Doctoral Degree in Bioinformatics at the Ludwig Maximilians Universität München, Germany • Affiliation: Cancer Research Center of SDU • Tel: 0531-88380202 • Email: [email protected] • Office: Dianjing Building, Rm.106, Baotuquan Campus 3 Introduction to Bioinformatics About this course • Schedule: 2011/9/14 - 2011/10/12, Mi. 14:00 - 18:00 • Locus: 8#, first floor, west, Computer Pool • Homepage: http://1.51.212.243/bioinfo.html • Table of Contents My name is Lampy. Chapter 1 : Introduction Chapter 2 : Databases Chapter 5 : Tree Chapter 3 : Alignment Chapter 4 : Structure 4 Introduction to Bioinformatics Literatures: 1. Bioinformatics - An Introduction, 2nd Edition, Jeremy Ramsden, 2009, Springer. 2. Bioinformatics For Dummies, 2nd Edition, Jean-Michel Claverie, Cedric Notredame, 2007, Wiley. 5 Introduction to Bioinformatics Information Page Vocabulary List Information Page Vocabulary Chapter 1, 2011/9/14 Chapter 1, 2011/9/14 Dr. rer. nat. Jing Gong Affiliation: Cancer Research Center of SDU FASTA FASTA Tel: 0531-88380202 FASTA (prounced FAST-Aye) FASTA (读作FAST-Aye) 代表 Email: [email protected] stands forFAST-ALL, reflecting FAST-ALL， 反映的实施是他能 Office: Dianjing Building, Rm.106, Baotuquan the fact that it canbe used for a 够用于快速的蛋白质比对或者快 Campus fast protein …… 组的核苷比对。该程序…… BLAST BLAST Schedule: 2011/9/14 - 2011/10/12, Mi. 14:00 - 18:00 Basic Local Alignment Search 基本局部比对搜索工具。以速度 Place: 8#, first floor, west, Computer Pool Tool. A sequence comparison 最优化算法为核心，搜索序列数 algorithm optimized for speed 据库得到最佳局部比对结果。用 Course Homepage: http://1.51.212.243/bioinfo.html used to search sequence 替代矩阵和查新序列…… dtabases …… Pubmed: http://www.ncbi.nlm.nih.gov/entrez/ Alignment ExPASy: http://expasy.org/ 比对 The result of a comparison of 两个甚至更多的基因或者蛋白质 NCBI: http://www.ncbi.nlm.nih.gov/ two or more gene or protein 序列进行比较的结果，用以计算 sequences in order to 他们碱基或者氨基酸的相似度。 PRI: http://pir.georgetown.edu determine their degree of base 序列比对用来决定两个甚至……. or amino acid……. 6 Introduction to Bioinformatics What is Bioinformatics? biophysics biohazards biometrics biomathematics biochemistry bioterrorism biopotato bioinformatics 7 Introduction to Bioinformatics What is Bioinformatics? Interdisciplinary a biology/medical researchers, just like you a professional in the pharmaceutical industry a policeman worrying about DNA testing a computer scientist developing bio-databases a consumer concerned about GMOs (Genetically Modified Organisms) …… 8 Introduction to Bioinformatics What is Bioinformatics? Definition: Bioinformatics – the science of collecting and analyzing complex biological data such as genetic codes. [Oxford Dictionary] Bioinformatics – the computational branch of molecular biology. [Bioinformatics for Dummies] Bioinformatics – the application of computer science and information technology to the field of biology and medicine. [Wikipedia] Bioinformatics – the science of how information is generated, transmitted, received, and interpreted in biological systems, i.e. the application of information science to biology. [Bioinformatics-An Introduction] A formel definition ? 9 Introduction to Bioinformatics History of Bioinformatics In 1809, French biologist Jean Baptiste Lamarck published “Philosophie Zoologique”. Lamarck stressed two main themes in his biological work: 1. The environment gives rise to changes in animals, i.e. changes through use and disuse. 2. Life was structured in an orderly manner and that many different parts of all bodies make it possible for the organic movements of animals. “blind as a mole” “show your teeth” “birds have no teeth?” Jean Baptiste Lamarck (1744-1829) 10 Introduction to Bioinformatics History of Bioinformatics In 1859, English naturalist Charles Darwin published “On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life”. Charles Darwin (1809-1882) 11 Introduction to Bioinformatics History of Bioinformatics In 1866, Austrian scientist Gregor Mendel demonstrated that the inheritance of certain traits in pea plants follows particular patterns, now referred to as the laws of Gregor J. Mendel (1822-1884) “Mendelian Inheritance”. 12 Introduction to Bioinformatics History of Bioinformatics In 1869, Swiss physician and biologist Friedrich Miescher isolated DNA from the white blood cells at Felix Hoppe-Seyler's laboratory at the University of Tübingen, Germany. Nuclei Nuclein Nucleic acid DNA Friedrich Miescher (1844-1895) 13 Introduction to Bioinformatics History of Bioinformatics Thomas Hunt Morgan, American geneticist, famous for his experimental research with the fruit fly by which he established the chromosome theory of heredity. He showed that genes are linked in a series on chromosomes and are responsible for identifiable, hereditary traits. Morgan’s work played a key role in establishing the field of genetics. He received the Nobel Prize for Physiology or Medicine in 1933. Thomas H. Morgen (1866-1945) nobel prize 1933 14 Introduction to Bioinformatics History of Bioinformatics In 1944, American physician and medical researcher Oswald Avery and his co-workers Colin MacLeod and Maclyn McCarty demonstrated that DNA is the material of which genes and chromosomes are made. In his experiment he destroyed the lipids, ribonucleic acids, carbohydrates, and proteins. Transformation still occurred after this. Next he destroyed the deoxyribonucleic acid. Transformation did not occur. Oswald Avery Colin MacLeod Maclyn McCarty (1877-1955) (1909-1972) (1911-2005) 15 Introduction to Bioinformatics History of Bioinformatics In 1950, American biochemist Erwin Chargaff noticed a pattern in the amounts of the four bases: adenine (A) , thymine (T) , cytosine (C) , guanine (G). He discovered that the amounts of adenine (A) and thymine (T) in DNA were roughly the same, as were the amounts of cytosine (C) and guanine (G). This later became known as Chargaff's rule. %A = %T and %G = %C Erwin Chargaff (1905-2002) 16 Introduction to Bioinformatics History of Bioinformatics In 1953, James D. Watson and Francis Crick suggested the first correct double-helix model of DNA structure in the journal Nature. Their double- helix model of DNA was based on a single X-ray diffraction image taken by Rosalind Franklin and Maurice Wilkins in 1952. James Waston Francis Crick Maurice Wilkins Rosalind Franklin (1928-) (1916-2004) (1916-2004) (1920-1958) nobel prize 1962 nobel prize 1962 nobel prize 1962 17 Introduction to Bioinformatics History of Bioinformatics The sequence of 77 nucleotides of a yeast alanine tRNA was found by an American biochemist Robert W. Holley in 1965. Holley was awarded the 1968 Nobel Prize in Physiology or Medicine for describing the structure of this tRNA, linking DNA and protein synthesis. Robert W. Holley (1922-1993) nobel prize 1968 18 Introduction to Bioinformatics History of Bioinformatics In 1977, Frederick Sanger and Colleagues introduced the “dideoxy” chain-termination method for sequencing DNA molecules, also known as the “Sanger method”. Hence, in 1980, he shared Nobel Prize in chemistry with Walter Gilbert. The key principle of the Sanger method was the use of dideoxynucleotide triphosphates Frederick Sanger Walter Gilbert (ddNTPs), as DNA chain terminators. (1918-) (1932-) nobel prize 1980 nobel prize 1980 19 Introduction to Bioinformatics History of Bioinformatics Read protein sequence directly in the DNA sequence! Central dogma of molecular biology was first articulated by Francis Crick in 1958 and re-stated Francis Crick in a Nature paper published in 1970. (1916-2004) 20 Introduction to Bioinformatics History of Bioinformatics Marshall Warren Nirenberg shared a Nobel Prize in Physiology or Medicine in 1968 with Har Gobind Khorana and Robert W. Holley for "breaking the genetic code" and describing how it operates in protein synthesis. Marshall Warren Har Gobind Robert W. Holley Nirenberg Khorana (1922-) (1922-1993) (1927-2010) nobel prize 1968 nobel prize 1968 nobel prize 1968 21 Introduction to Bioinformatics English Courses for Graduate Students History of Bioinformatics Amino acids are the building blocks of protein. Protein is a nutrient needed by the human body for growth and maintenance. Amino acids are made of carbon, hydrogen, oxygen, nitrogen, and sulfur atoms. A protein = C1200H2400O600N300S100 22 Introduction to Bioinformatics English Courses for Graduate Students History of Bioinformatics insulin = ( # 1-letter 3-letter Nmae A given type of protein 30 glycines + 1 A Ala Alanine 44 alanines + 2 R Arg Arginine always contains the same 5 tyrosines + 3 N Asn Asparagine number of total amino acids 14 glutamines 4 D Asp Aspartic acid + . .) 5 C Cys Cysteine in the same proportion. 6 Q Gln Glutamine 7 E Glu Glutamic acid 8 G Gly Glycine Amino acids are linked 9 H His Histindine together as a chain. 10 I Ile Isoleucine The first amino acid 11 L Leu Leucine 12 K Lys Lysine sequence of a protein, 13 M Met Methionine Insulin, was determined 14 F Phe Phenylalanine Frederick Sanger (1918-) in 1951 by Dr. Sanger. nobel prize 1958 15 P Pro Proline 16 S Ser Serine 17 T Thr Threonine insulin = MALWMRLLPLLALLALWGPDPAAAFVNQHLCGSHL 18 W Trp Trytophan VEALYLVCGERGFFYTPKTRREAEDLQVGQVELGGGPGAGSLQPL
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