《生物信息学》教学课件.ppt

Introduction to Bioinformatics1 2 People with very diverse backgrounds in biology Some people with backgrounds in computer science and biostatistics Most people (will) have a favorite gene, protein, or disease, or a high throughput datasetWho is taking this course?3 Different user needs, different approachesweb-based or graphical user interface (GUI)command lineNCBIEBI,centralresourcesUCSC,EnsemblgenomebrowsersGalaxy: webimplementationof browser data,NGS toolsPerl, R:manipulate data filesLinux:next-generation sequencing, other toolsSoftware for data analysis, large databasesPartekMEGA5RStudio4 To provide an introduction to bioinformatics with a focus on the National Center for Biotechnology Information (NCBI), UCSC, and EBI To focus on the analysis of DNA, RNA and proteins To introduce you to the analysis of genomes To combine theory and practice to help you solve research problemsWhat are the goals of the course?5 Suppose we are interested in learning about beta globin (HBB), a subunit of hemoglobin NCBI offers information at the levels of DNA (e.g. variation in disease), RNA (e.g. gene expression data from microarrays), protein (e.g. 3D structure), pathways EBI offers comparable information Other portals such as ExPASy offer hundreds of analysis toolsWorkflow #1: How do we analyze a protein?6 Choose an individual (e.g. a patient), obtain informed consent, get blood, purify genomic DNA Obtain raw DNA reads by next-generation sequencing Align the reads to a reference human genome Call variants (single nucleotide variants, indels) Determine the functional significance of variants (deleterious or neutral) Workflow #2: How do we analyze a human genome?7 TextbookThe 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 everyone.You can also purchase a copy at the bookstore