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The bestselling introduction to bioinformatics and genomics - now in its third edition Widely received in its previous editions, Bioinformatics and Functional Genomics offers the most broad-based introduction to this explosive new discipline. Now in a thoroughly updated and expanded third edition, it continues to be the go-to source for students and professionals involved in biomedical research. This book provides up-to-the-minute coverage of the fields of bioinformatics and genomics. Features new to this edition include: * Extensive revisions and a slight reorder of chapters for a more effective organization * A brand new chapter on next-generation sequencing * An expanded companion website, also updated as and when new information becomes available * Greater emphasis on a computational approach, with clear guidance of how software tools work and introductions to the use of command-line tools such as software for next-generation sequence analysis, the R programming language, and NCBI search utilities The book is complemented by lavish illustrations and more than 500 figures and tables - many newly-created for the third edition to enhance clarity and understanding. Each chapter includes learning objectives, a problem set, pitfalls section, boxes explaining key techniques and mathematics/statistics principles, a summary, recommended reading, and a list of freely available software. Readers may visit a related Web page for supplemental information such as PowerPoints and audiovisual files of lectures, and videocasts of how to perform many basic operations: www.wiley.com/go/pevsnerbioinformatics. Bioinformatics and Functional Genomics, Third Edition serves as an excellent single-source textbook for advanced undergraduate and beginning graduate-level courses in the biological sciences and computer sciences. It is also an indispensable resource for biologists in a broad variety of disciplines who use the tools of bioinformatics and genomics to study particular research problems; bioinformaticists and computer scientists who develop computer algorithms and databases; and medical researchers and clinicians who want to understand the genomic basis of viral, bacterial, parasitic, or other diseases.
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Seitenzahl: 2747
Veröffentlichungsjahr: 2015
Third Edition
Jonathan Pevsner
Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland, USA and Department of Psychiatry and Behavioral Sciences, The Johns Hopkins School of Medicine, Baltimore, Maryland, USA
This edition first published 2015 © 2015 by John Wiley & Sons Inc
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Library of Congress Cataloging-in-Publication DataPevsner, Jonathan, 1961- , author. Bioinformatics and functional genomics / Jonathan Pevsner.—Third edition. p. ; cm. Includes bibliographical references and indexes. ISBN 978-1-118-58178-0 (cloth) I. Title. [DNLM: 1. Computational Biology—methods. 2. Genomics. 3. Genetic Techniques. 4. Proteomics. QU 26.5] QH441.2 572.8′6–dc23
2015014465
A catalogue record for this book is available from the British Library.
Wiley also publishes its books in a variety of electronic formats. Some content that appears in print may not be available in electronic books.
The cover image is by Leonardo da Vinci, a study of a man in profile with studies of horse and riders (reproduced with kind permission of the Gallerie d’Accademia, Venice, Ms. 7r [236r], pen, black and red chalk). To the upper right a DNA molecule is shown (image courtesy of Wikimedia Commons) and a protein (human serum albumin, the most abundant protein in blood plasma, accession 1E7I, visualized with Cn3D software described in Chapter 13). Leonardo’s text reads: “From the eyebrow to the junction of the lip with the chin, and the angle of the jaw and the upper angle where the ear joins the temple will be a perfect square. And each side by itself is half the head. The hollow of the cheek bone occurs half way between the tip of the nose and the top of the jaw bone, which is the lower angle of the setting on of the ear, in the frame here represented. From the angle of the eye-socket to the ear is as far as the length of the ear, or the third of the face.” (Translation by Jean-Paul Richter, The Notebooks of Leonardo da Vinci, London, 1883.)
For three generations of family: to my parents Aihud and Lucille; to my wife Barbara; to my daughters Kim, Ava, and Lillian; and to my niece Madeline
Preface to the Third Edition
About the Companion Website
PART I ANALYZING DNA, RNA, AND PROTEIN SEQUENCES
CHAPTER 1 Introduction
ORGANIZATION OF THE BOOK
BIOINFORMATICS: THE BIG PICTURE
ORGANIZATION OF THE CHAPTERS
SUGGESTIONS FOR STUDENTS AND TEACHERS: EXERCISES, FIND-A-GENE, AND CHARACTERIZE-A-GENOME
BIOINFORMATICS SOFTWARE: TWO CULTURES
BIOINFORMATICS AND OTHER INFORMATICS DISCIPLINES
ADVICE FOR STUDENTS
SUGGESTED READING
REFERENCES
CHAPTER 2 Access to Sequence Data and Related Information
INTRODUCTION TO BIOLOGICAL DATABASES
CENTRALIZED DATABASES STORE DNA SEQUENCES
CONTENTS OF DNA, RNA, AND PROTEIN DATABASES
CENTRAL BIOINFORMATICS RESOURCES: NCBI AND EBI
ACCESS TO INFORMATION: ACCESSION NUMBERS TO LABEL AND IDENTIFY SEQUENCES
ACCESS TO INFORMATION VIA GENE RESOURCE AT NCBI
COMMAND-LINE ACCESS TO DATA AT NCBI
ACCESS TO INFORMATION: GENOME BROWSERS
EXAMPLES OF HOW TO ACCESS SEQUENCE DATA: INDIVIDUAL GENES/PROTEINS
HOW TO ACCESS SETS OF DATA: LARGE-SCALE QUERIES OF REGIONS AND FEATURES
ACCESS TO BIOMEDICAL LITERATURE
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 3 Pairwise Sequence Alignment
INTRODUCTION
SCORING MATRICES
ALIGNMENT ALGORITHMS: GLOBAL AND LOCAL
THE STATISTICAL SIGNIFICANCE OF PAIRWISE ALIGNMENTS
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 4 Basic Local Alignment Search Tool (BLAST)
INTRODUCTION
BLAST SEARCH STEPS
BLAST ALGORITHM USES LOCAL ALIGNMENT SEARCH STRATEGY
BLAST SEARCH STRATEGIES
USING BLAST FOR GENE DISCOVERY: FIND-A-GENE
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 5 Advanced Database Searching
INTRODUCTION
SPECIALIZED BLAST SITES
FINDING DISTANTLY RELATED PROTEINS: POSITION-SPECIFIC ITERATED BLAST (PSI-BLAST) AND DELTA-BLAST
PROFILE SEARCHES: HIDDEN MARKOV MODELS
BLAST-LIKE ALIGNMENT TOOLS TO SEARCH GENOMIC DNA RAPIDLY
ALIGNING NEXT-GENERATION SEQUENCE (NGS) READS TO A REFERENCE GENOME
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 6 Multiple Sequence Alignment
INTRODUCTION
FIVE MAIN APPROACHES TO MULTIPLE SEQUENCE ALIGNMENT
BENCHMARKING STUDIES: APPROACHES, FINDINGS, CHALLENGES
DATABASES OF MULTIPLE SEQUENCE ALIGNMENTS
MULTIPLE SEQUENCE ALIGNMENTS OF GENOMIC REGIONS
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 7 Molecular Phylogeny and Evolution
INTRODUCTION TO MOLECULAR EVOLUTION
PRINCIPLES OF MOLECULAR PHYLOGENY AND EVOLUTION
MOLECULAR PHYLOGENY: PROPERTIES OF TREES
TYPE OF TREES
FIVE STAGES OF PHYLOGENETIC ANALYSIS
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
PART II GENOMEWIDE ANALYSIS OF DNA, RNA, AND PROTEIN
CHAPTER 8 DNA: The Eukaryotic Chromosome
INTRODUCTION
GENERAL FEATURES OF EUKARYOTIC GENOMES AND CHROMOSOMES
REPETITIVE DNA CONTENT OF EUKARYOTIC CHROMOSOMES
GENE CONTENT OF EUKARYOTIC CHROMOSOMES
REGULATORY REGIONS OF EUKARYOTIC CHROMOSOMES
COMPARISON OF EUKARYOTIC DNA
VARIATION IN CHROMOSOMAL DNA
TECHNIQUES TO MEASURE CHROMOSOMAL CHANGE
PERSPECTIVE
PITFALLS
ADVICE TO STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 9 Analysis of Next-Generation Sequence Data
INTRODUCTION
DNA SEQUENCING TECHNOLOGIES
ANALYSIS OF NEXT-GENERATION SEQUENCING OF GENOMIC DNA
SPECIALIZED APPLICATIONS OF NEXT-GENERATION SEQUENCING
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 10 Bioinformatic Approaches to Ribonucleic Acid (RNA)
INTRODUCTION TO RNA
NONCODING RNA
INTRODUCTION TO MESSENGER RNA
MICROARRAYS AND RNA-SEQ: GENOME-WIDE MEASUREMENT OF GENE EXPRESSION
INTERPRETATION OF RNA ANALYSES
PERSPECTIVE
PITFALLS
ADVICE TO STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 11 Gene Expression: Microarray and RNA-seq Data Analysis
INTRODUCTION
MICROARRAY ANALYSIS METHOD 1: GEO2R AT NCBI
MICROARRAY ANALYSIS METHOD 2: PARTEK
MICROARRAY ANALYSIS METHOD 3: ANALYZING A GEO DATASET WITH R
MICROARRAY DATA ANALYSIS: DESCRIPTIVE STATISTICS
RNA-SEQ
FUNCTIONAL ANNOTATION OF MICROARRAY DATA
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 12 Protein Analysis and Proteomics
INTRODUCTION
TECHNIQUES FOR IDENTIFYING PROTEINS
FOUR PERSPECTIVES ON PROTEINS
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 13 Protein Structure
OVERVIEW OF PROTEIN STRUCTURE
PRINCIPLES OF PROTEIN STRUCTURE
PROTEIN DATA BANK
PROTEIN STRUCTURE PREDICTION
INTRINSICALLY DISORDERED PROTEINS
PROTEIN STRUCTURE AND DISEASE
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 14 Functional Genomics
INTRODUCTION TO FUNCTIONAL GENOMICS
EIGHT MODEL ORGANISMS FOR FUNCTIONAL GENOMICS
FUNCTIONAL GENOMICS USING REVERSE AND FORWARD GENETICS
FUNCTIONAL GENOMICS AND THE CENTRAL DOGMA
PROTEOMICS APPROACHES TO FUNCTIONAL GENOMICS
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
PART III GENOMEWIDE ANALYSIS
CHAPTER 15 Genomes Across the Tree of Life
INTRODUCTION
PROMINENT WEB RESOURCES
GENOME-SEQUENCING PROJECTS: CHRONOLOGY
GENOME ANALYSIS PROJECTS: INTRODUCTION
GENOME ANALYSIS PROJECTS: SEQUENCING
GENOME ANALYSIS PROJECTS: ASSEMBLY
GENOME ANALYSIS PROJECTS: ANNOTATION
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 16 Completed Genomes: Viruses
INTRODUCTION
CLASSIFICATION OF VIRUSES
BIOINFORMATICS APPROACHES TO PROBLEMS IN VIROLOGY
HUMAN IMMUNODEFICIENCY VIRUS (HIV)
INFLUENZA VIRUS
MEASLES VIRUS
EBOLA VIRUS
HERPESVIRUS: FROM PHYLOGENY TO GENE EXPRESSION
GIANT VIRUSES
PERSPECTIVES
PITFALLS
ADVICE FOR STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 17 Completed Genomes: Bacteria and Archaea
INTRODUCTION
CLASSIFICATION OF BACTERIA AND ARCHAEA
THE HUMAN MICROBIOME
ANALYSIS OF BACTERIAL AND ARCHAEAL GENOMES
COMPARISON OF BACTERIAL GENOMES
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 18 Eukaryotic Genomes: Fungi
INTRODUCTION
DESCRIPTION AND CLASSIFICATION OF FUNGI
INTRODUCTION TO BUDDING YEAST
SACCHAROMYCES CEREVISIAE
GENE DUPLICATION AND GENOME DUPLICATION OF
S. CEREVISIAE
COMPARATIVE ANALYSES OF HEMIASCOMYCETES
ANALYSIS OF FUNGAL GENOMES
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 19 Eukaryotic Genomes: From Parasites to Primates
INTRODUCTION
PROTOZOANS AT BASE OF TREE LACKING MITOCHONDRIA
GENOMES OF UNICELLULAR PATHOGENS: TRYPANOSOMES AND
LEISHMANIA
THE CHROMALVEOLATES
PLANT GENOMES
SLIME AND FRUITING BODIES AT THE FEET OF METAZOANS
METAZOANS
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
WEB RESOURCES
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 20 Human Genome
INTRODUCTION
MAIN CONCLUSIONS OF HUMAN GENOME PROJECT
GATEWAYS TO ACCESS THE HUMAN GENOME
HUMAN GENOME PROJECT
25 HUMAN CHROMOSOMES
HUMAN GENOME VARIATION
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
CHAPTER 21 Human Disease
HUMAN GENETIC DISEASE: A CONSEQUENCE OF DNA VARIATION
CATEGORIES OF DISEASE
DISEASE DATABASES
APPROACHES TO IDENTIFYING DISEASE-ASSOCIATED GENES AND LOCI
HUMAN DISEASE GENES IN MODEL ORGANISMS
FUNCTIONAL CLASSIFICATION OF DISEASE GENES
PERSPECTIVE
PITFALLS
ADVICE FOR STUDENTS
DISCUSSION QUESTIONS
SELF-TEST QUIZ
SUGGESTED READING
REFERENCES
Glossary
Self-Test Quiz: Solutions
Author Index
Subject Index
EULA
Chapter 1
Table 1.1
Table 1.2
Chapter 2
Table 2.1
Table 2.2
Table 2.3
Table 2.4
Table 2.5
Table 2.6
Table 2.7
Table 2.8
Table 2.9
Table 2.10
Table 2.11
Chapter 3
Table 3.1
Table 3.2
Table 3.3
Table 3.4
Table 3.5
Chapter 4
Table 4.1
Table 4.2
Table 4.3
Chapter 5
Table 5.1
Table 5.2
Chapter 6
Table 6.1
Chapter 7
Table 7.1
Chapter 8
Table 8.1
Table 8.2
Table 8.3
Table 8.4
Table 8.5
Table 8.6
Table 8.7
Table 8.8
Table 8.9
Chapter 9
Table 9.1
Table 9.2
Table 9.3
Table 9.4
Table 9.5
Table 9.6
Chapter 10
Table 10.1
Table 10.2
Table 10.3
Table 10.4
Table 10.5
Table 10.6
Table 10.7
Table 10.8
Table 10.9
Chapter 11
Table 11.1
Table 11.2
Table 11.3
Table 11.4
Chapter 12
Table 12.1
Table 12.2
Table 12.3
Table 12.4
Table 12.5
Table 12.6
Table 12.7
Table 12.8
Table 12.9
Table 12.10
Table 12.11
Table 12.12
Table 12.13
Table 12.14
Table 12.15
Table 12.16
Table 12.17
Chapter 13
Table 13.1
Table 13.2
Table 13.3
Table 13.4
Table 13.5
Table 13.6
Table 13.7
Table 13.8
Table 13.9
Table 13.10
Chapter 14
Table 14.1
Table 14.2
Table 14.3
Chapter 15
Table 15.1
Table 15.2
Table 15.3
Table 15.4
Table 15.5
Table 15.6
Table 15.7
Table 15.8
Chapter 16
Table 16.1
Table 16.2
Table 16.3
Table 16.4
Table 16.5
Table 16.6
Table 16.7
Chapter 17
Table 17.1
Table 17.2
Table 17.3
Table 17.4
Table 17.5
Table 17.6
Table 17.7
Table 17.8
Table 17.9
Chapter 18
Table 18.1
Table 18.2
Table 18.3
Table 18.4
Table 18.5
Table 18.6
Chapter 19
Table 19.1
Table 19.2
Table 19.3
Chapter 20
Table 20.1
Table 20.2
Table 20.3
Table 20.4
Table 20.5
Table 20.6
Table 20.7
Table 20.8
Table 20.9
Table 20.10
Table 20.11
Table 20.12
Table 20.13
Table 20.14
Table 20.15
Table 20.16
Table 20.17
Table 20.18
Table 20.19
Table 20.20
Chapter 21
Table 21.1
Table 21.2
Table 21.3
Table 21.4
Table 21.5
Table 21.6
Table 21.7
Table 21.8
Table 21.9
Table 21.10
Table 21.11
Table 21.12
Table 21.13
Table 21.14
Table 21.15
Table 21.16
Table 21.17