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1、Introduction to BioinformaticsMonday, November 15, 2010 Jonathan Pevsner pevsnerkennedykrieger.org Bioinformatics M.E:800.707,People with very diverse backgrounds in biology Some people with backgrounds in computerscience and biostatisticsMost people (will) have a favorite gene, protein, or disease,
2、Who is taking this course?,To provide an introduction to bioinformatics witha focus on the National Center for BiotechnologyInformation (NCBI), UCSC, and EBITo focus on the analysis of DNA, RNA and proteinsTo introduce you to the analysis of genomesTo combine theory and practice to help you solve re
3、search problems,What are the goals of the course?,Textbook,The course textbook has no required textbook. I wrote Bioinformatics and Functional Genomics (Wiley-Blackwell, 2nd edition 2009). The lectures in this course correspond closely to chapters. I will make pdfs of the chapters available to every
4、one.You can also purchase a copy at the bookstore, at (now $60), or at Wiley with a 20% discount through the books website www.bioinfbook.org.,Web sites,The course website is reached via moodle:http:/pevsnerlab.kennedykrieger.org/moodle(or Google “moodle bioinformatics”)-This site contains the powe
5、rpoints for each lecture,including black & white versions for printing-The weekly quizzes are here-You can ask questions via the forum-Audio files of each lecture will be posted hereThe textbook website is:http:/www.bioinfbook.orgThis has powerpoints, URLs, etc. organized by chapter. This is most us
6、eful to find “web documents” corresponding to each chapter.,Literature references,You are encouraged to read original source articles (posted on moodle). They will enhance your understanding of the material. Readings are optional but recommended.,Themes throughout the course: the beta globin gene/pr
7、otein family,We will use beta globin as a model gene/protein throughout the course. Globins including hemoglobin and myoglobin carry oxygen. We will study globins in a variety of contexts including-sequence alignment-gene expression-protein structure-phylogeny-homologs in various species,Computer la
8、bs,There are no computer labs, but the seven weekly quizzes function as a computer lab. To solve the questions, you will need to go to websites, use databases, and use software.,Grading,60% moodle quizzes (your top 6 out of 7 quizzes). Quizzes are taken at the moodle website, andare due one week aft
9、er the relevant lecture. Special extended due date for quizzes due immediately after Thanksgiving and the New Year.40% final exam Monday, January 10 (in class).Closed book, cumulative, no computer,short answer / multiple choice. Past exams will be made available ahead of time.,Google “moodle bioinfo
10、rmatics” to get here; Click “Bioinformatics” to sign in; The enrollment key you need is,The password to get the book chapter pdf is,Outline for the course (all on Mondays),1. Accessing information about DNA and proteins Nov. 15 2. Pairwise alignment Nov. 22 3. BLAST Nov. 29 4. Multiple sequence alig
11、nment Dec. 6 5. Molecular phylogeny and evolution Dec. 13 6. Microarrays Dec. 20 7. Genomes Jan. 3 Final exam Jan. 10,Outline for today,Definition of bioinformaticsOverview of the NCBI websiteAccessing information: accession numbers and RefSeqEntrez Gene (and UniGene, HomoloGene)Protein Databases: U
12、niProt, ExPASyThree genome browsers: NCBI, UCSC, EnsemblAccess to biomedical literature,Interface of biology and computersAnalysis of proteins, genes and genomesusing computer algorithms and computer databasesGenomics is the analysis of genomes. The tools of bioinformatics are used to make sense of
13、the billions of base pairs of DNA that are sequenced by genomics projects.,What is bioinformatics?,On bioinformatics,“Science is about building causal relations between natural phenomena (for instance, between a mutation in a gene and a disease). The development of instruments to increase our capaci
14、ty to observe natural phenomena has, therefore, played a crucial role in the development of science - the microscope being the paradigmatic example in biology. With the human genome, the natural world takes an unprecedented turn: it is better described as a sequence of symbols. Besides high-throughp
15、ut machines such as sequencers and DNA chip readers, the computer and the associated software becomes the instrument to observe it, and the discipline of bioinformatics flourishes.”,On bioinformatics,“However, as the separation between us (the observers) and the phenomena observed increases (from or
16、ganism to cell to genome, for instance), instruments may capture phenomena only indirectly, through the footprints they leave. Instruments therefore need to be calibrated: the distance between the reality and the observation (through the instrument) needs to be accounted for. This issue of Genome Bi
17、ology is about calibrating instruments to observe gene sequences; more specifically, computer programs to identify human genes in the sequence of the human genome.”Martin Reese and Roderic Guig, Genome Biology 2006 7(Suppl I):S1, introducing EGASP, the Encyclopedia of DNA Elements (ENCODE) Genome Annotation Assessment Project,
