Developing Bioinformatics Computer Skills.Pdf
Total Page:16
File Type:pdf, Size:1020Kb
Safari | Developing Bioinformatics Computer Skills Show TOC | Frames My Desktop | Account | Log Out | Subscription | Help Programming > Developing Bioinformatics Computer Skills See All Titles Developing Bioinformatics Computer Skills Cynthia Gibas Per Jambeck Publisher: O'Reilly First Edition April 2001 ISBN: 1-56592-664-1, 446 pages Buy Print Version Developing Bioinformatics Computer Skills will help biologists, researchers, and students develop a structured approach to biological data and the computer skills they'll need to analyze it. The book covers Copyright the Unix file system, building tools and databases for bioinformatics, Table of Contents computational approaches to biological problems, an introduction to Index Perl for bioinformatics, data mining, data visualization, and tips for Full Description tailoring data analysis software to individual research needs. About the Author Reviews Reader reviews Errata Delivered for Maurice ling Last updated on 10/30/2001 Swap Option Available: 7/15/2002 Developing Bioinformatics Computer Skills, © 2002 O'Reilly © 2002, O'Reilly & Associates, Inc. http://safari.oreilly.com/main.asp?bookname=bioskills [6/2/2002 8:49:35 AM] Safari | Developing Bioinformatics Computer Skills Show TOC | Frames My Desktop | Account | Log Out | Subscription | Help Programming > Developing Bioinformatics Computer Skills See All Titles Developing Bioinformatics Computer Skills Copyright © 2001 O'Reilly & Associates, Inc. All rights reserved. Printed in the United States of America. Published by O'Reilly & Associates, Inc., 1005 Gravenstein Highway North, Sebastopol, CA 95472. O'Reilly & Associates books may be purchased for educational, business, or sales promotional use. Online editions are also available for most titles (http://safari.oreilly.com). For more information contact our corporate/institutional sales department: 800-998-9938 or corporate@oreilly.com. The O'Reilly logo is a registered trademark of O'Reilly & Associates, Inc. Many of the designations used by manufacturers and sellers to distinguish their products are claimed as trademarks. Where those designations appear in this book, and O'Reilly & Associates, Inc. was aware of a trademark claim, the designations have been printed in caps or initial caps. The association between the image of a Caenorhabditis elegans and the topic of bioinformatics is a trademark of O'Reilly & Associates, Inc. While every precaution has been taken in the preparation of this book, the publisher assumes no responsibility for errors or omissions, or for damages resulting from the use of the information contained herein. Delivered for Maurice ling Last updated on 10/30/2001 Swap Option Available: 7/15/2002 Developing Bioinformatics Computer Skills, © 2002 O'Reilly © 2002, O'Reilly & Associates, Inc. http://safari.oreilly.com/main.asp?bookname=bioskills&mode=3 [6/2/2002 8:49:49 AM] Safari | Developing Bioinformatics Computer Skills Show TOC | Frames My Desktop | Account | Log Out | Subscription | Help Programming > Developing Bioinformatics Computer Skills See All Titles Developing Bioinformatics Computer Skills Preface Audience for This Book Structure of This Book Our Approach to Bioinformatics URLs Referenced in This Book Conventions Used in This Book Comments and Questions Acknowledgments I: Introduction 1. Biology in the Computer Age 1.1 How Is Computing Changing Biology? 1.2 Isn't Bioinformatics Just About Building Databases? 1.3 What Does Informatics Mean to Biologists? 1.4 What Challenges Does Biology Offer Computer Scientists? 1.5 What Skills Should a Bioinformatician Have? 1.6 Why Should Biologists Use Computers? 1.7 How Can I Configure a PC to Do Bioinformatics Research? 1.8 What Information and Software Are Available? 1.9 Can I Learn a Programming Language Without Classes? 1.10 How Can I Use Web Information? 1.11 How Do I Understand Sequence Alignment Data? 1.12 How Do I Write a Program to Align Two Biological Sequences? 1.13 How Do I Predict Protein Structure from Sequence? 1.14 What Questions Can Bioinformatics Answer? 2. Computational Approaches to Biological Questions 2.1 Molecular Biology's Central Dogma 2.2 What Biologists Model 2.3 Why Biologists Model 2.4 Computational Methods Covered in This Book 2.5 A Computational Biology Experiment II: The Bioinformatics Workstation 3. Setting Up Your Workstation 3.1 Working on a Unix System 3.2 Setting Up a Linux Workstation 3.3 How to Get Software Working 3.4 What Software Is Needed? 4. Files and Directories in Unix 4.1 Filesystem Basics 4.2 Commands for Working with Directories and Files 4.3 Working in a Multiuser Environment http://safari.oreilly.com/main.asp?bookname=bioskills&mode=1 (1 of 4) [6/2/2002 8:49:58 AM] Safari | Developing Bioinformatics Computer Skills 5. Working on a Unix System 5.1 The Unix Shell 5.2 Issuing Commands on a Unix System 5.3 Viewing and Editing Files 5.4 Transformations and Filters 5.5 File Statistics and Comparisons 5.6 The Language of Regular Expressions 5.7 Unix Shell Scripts 5.8 Communicating with Other Computers 5.9 Playing Nicely with Others in a Shared Environment III: Tools for Bioinformatics 6. Biological Research on the Web 6.1 Using Search Engines 6.2 Finding Scientific Articles 6.3 The Public Biological Databases 6.4 Searching Biological Databases 6.5 Depositing Data into the Public Databases 6.6 Finding Software 6.7 Judging the Quality of Information 7. Sequence Analysis, Pairwise Alignment, and Database Searching 7.1 Chemical Composition of Biomolecules 7.2 Composition of DNA and RNA 7.3 Watson and Crick Solve the Structure of DNA 7.4 Development of DNA Sequencing Methods 7.5 Genefinders and Feature Detection in DNA 7.6 DNA Translation 7.7 Pairwise Sequence Comparison 7.8 Sequence Queries Against Biological Databases 7.9 Multifunctional Tools for Sequence Analysis 8. Multiple Sequence Alignments, Trees, and Profiles 8.1 The Morphological to the Molecular 8.2 Multiple Sequence Alignment 8.3 Phylogenetic Analysis 8.4 Profiles and Motifs 9. Visualizing Protein Structures and Computing Structural Properties 9.1 A Word About Protein Structure Data 9.2 The Chemistry of Proteins 9.3 Web-Based Protein Structure Tools 9.4 Structure Visualization 9.5 Structure Classification 9.6 Structural Alignment 9.7 Structure Analysis 9.8 Solvent Accessibility and Interactions 9.9 Computing Physicochemical Properties 9.10 Structure Optimization 9.11 Protein Resource Databases 9.12 Putting It All Together 10. Predicting Protein Structure and Function from Sequence 10.1 Determining the Structures of Proteins 10.2 Predicting the Structures of Proteins 10.3 From 3D to 1D http://safari.oreilly.com/main.asp?bookname=bioskills&mode=1 (2 of 4) [6/2/2002 8:49:58 AM] Safari | Developing Bioinformatics Computer Skills 10.4 Feature Detection in Protein Sequences 10.5 Secondary Structure Prediction 10.6 Predicting 3D Structure 10.7 Putting It All Together: A Protein Modeling Project 10.8 Summary 11. Tools for Genomics and Proteomics 11.1 From Sequencing Genes to Sequencing Genomes 11.2 Sequence Assembly 11.3 Accessing Genome Informationon the Web 11.4 Annotating and Analyzing Whole Genome Sequences 11.5 Functional Genomics: New Data Analysis Challenges 11.6 Proteomics 11.7 Biochemical Pathway Databases 11.8 Modeling Kinetics and Physiology 11.9 Summary IV: Databases and Visualization 12. Automating Data Analysis with Perl 12.1 Why Perl? 12.2 Perl Basics 12.3 Pattern Matching and Regular Expressions 12.4 Parsing BLAST Output Using Perl 12.5 Applying Perl to Bioinformatics 13. Building Biological Databases 13.1 Types of Databases 13.2 Database Software 13.3 Introduction to SQL 13.4 Installing the MySQL DBMS 13.5 Database Design 13.6 Developing Web-Based Software That Interacts with Databases 14. Visualization and Data Mining 14.1 Preparing Your Data 14.2 Viewing Graphics 14.3 Sequence Data Visualization 14.4 Networks and Pathway Visualization 14.5 Working with Numerical Data 14.6 Visualization: Summary 14.7 Data Mining and Biological Information Bibliography Unix SysAdmin Perl General Reference Bioinformatics Reference Molecular Biology/Biology Reference Protein Structure and Biophysics Genomics Biotechnology Databases Visualization Data Mining http://safari.oreilly.com/main.asp?bookname=bioskills&mode=1 (3 of 4) [6/2/2002 8:49:58 AM] Safari | Developing Bioinformatics Computer Skills Colophon Delivered for Maurice ling Last updated on 10/30/2001 Swap Option Available: 7/15/2002 Developing Bioinformatics Computer Skills, © 2002 O'Reilly © 2002, O'Reilly & Associates, Inc. http://safari.oreilly.com/main.asp?bookname=bioskills&mode=1 (4 of 4) [6/2/2002 8:49:58 AM] Safari | Developing Bioinformatics Computer Skills -> Preface Show TOC | Frames My Desktop | Account | Log Out | Subscription | Help Programming > Developing Bioinformatics Computer Skills > Preface See All Titles Make Note | Bookmark CONTINUE > 158127045003020048038218232180015152050067001135112006120215207095121041242031111020227 Preface Computers and the World Wide Web are rapidly and dramatically changing the face of biological research. These days, the term "paradigm shift" is used to describe everything from new business trends to new flavors of cola, but biological science is in the midst of a paradigm shift in the classical sense. Theoretical and computational biology have existed for decades on the "fringe" of biological science. But within just a few short years, the flood of new biological data produced by genomics efforts and, by necessity, the application of computers to the analysis of this genomic data, has begun to affect every aspect of the biological sciences. Research that used to start in the laboratory now starts at the computer, as scientists search databases for information that might suggest new hypotheses. In the last two decades, both personal computers and supercomputers have become accessible to scientists across all disciplines. Personal computers have developed from expensive novelties with little real computing power into machines that are as powerful as the supercomputers of 10 years ago. Just as they've replaced the author's typewriter and the accountant's ledger, computers have taken their place in controlling and collecting data from lab equipment.