Bioinformatics and Functional Genomics - Jonathan Pevsner - E-Book

Bioinformatics and Functional Genomics E-Book

Jonathan Pevsner

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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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Bioinformatics and Functional Genomics

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

Registered office: John Wiley & Sons, Ltd, The Atrium, Southern Gate, Chichester, West Sussex, PO19 8SQ, UK

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The right of the author to be identified as the author of this work has been asserted in accordance with the UK Copyright, Designs and Patents Act 1988.

All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording or otherwise, except as permitted by the UK Copyright, Designs and Patents Act 1988, without the prior permission of the publisher.

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Limit of Liability/Disclaimer of Warranty: While the publisher and author(s) have used their best efforts in preparing this book, they make no representations or warranties with respect to the accuracy or completeness of the contents of this book and specifically disclaim any implied warranties of merchantability or fitness for a particular purpose. It is sold on the understanding that the publisher is not engaged in rendering professional services and neither the publisher nor the author shall be liable for damages arising herefrom. If professional advice or other expert assistance is required, the services of a competent professional should be sought.

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

Contents

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

List of Tables

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