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COMPUTER SKILS
Content
Preface
__________________________________________________________6
Audience for This Book_______________________________________6
Structure of This Book________________________________________7
Our Approach to Bioinformatics________________________________9
URLs Referenced in This Book________________________________________9
Conventions Used in This Book________________________________________9
Comments and Questions________________________________________9
Acknowledgments________________________________________10
Chapter 1. Biology in the Computer Age________________________________________11
1.1 How Is Computing Changing Biology? ________________________________________11
1.2 Isn't Bioinformatics Just About Building Databases? ________________________________________15
1.3 What Does Informatics Mean to Biologists? ________________________________________18
1.4 What Challenges Does Biology Offer Computer Scientists? ________________________________________18
1.5 What Skills Should a Bioinformatician Have? ________________________________________19
1.6 Why Should Biologists Use Computers? ________________________________________20
1.7 How Can I Configure a PC to Do Bioinformatics Research? ________________________________________21
1.8 What Information and Software Are Available? ________________________________________22
1.9 Can I Learn a Programming Language Without Classes? ________________________________________23
1.10 How Can I Use Web Information? ________________________________________23
1.11 How Do I Understand Sequence Alignment Data? ________________________________________24
1.12 How Do I Write a Program to Align Two Biological Sequences? ___________________________________24
1.13 How Do I Predict Protein Structure from Sequence? ________________________________________24
1.14 What Questions Can Bioinformatics Answer? ________________________________________24
Chapter 2. Computational Approaches to Biological Questions________________________________________26
2.1 Molecular Biology's Central Dogma________________________________________26
2.2 What Biologists Model________________________________________30
2.3 Why Biologists Model________________________________________33
2.4 Computational Methods Covered in This Book________________________________________34
2.5 A Computational Biology Experiment________________________________________38
Chapter 3. Setting Up Your Workstation________________________________________44
3.1 Working on a Unix System________________________________________44
3.2 Setting Up a Linux Workstation________________________________________46
3.3 How to Get Software Working________________________________________51
3.4 What Software Is Needed? ________________________________________57
Chapter 4. Files and Directories in Unix________________________________________58
4.1 Filesystem Basics________________________________________58
4.2 Commands for Working with Directories and Files________________________________________63
4.3 Working in a Multiuser Environment________________________________________70
5. Working on a Unix System________________________________________78
5.1 The Unix Shell________________________________________78
5.2 Issuing Commands on a Unix System________________________________________79
5.3 Viewing and Editing Files________________________________________84
5.4 Transformations and Filters________________________________________90
5.5 File Statistics and Comparisons________________________________________97
5.6 The Language of Regular Expressions________________________________________99
5.7 Unix Shell Scripts________________________________________102
5.8 Communicating with Other Computers________________________________________103
5.9 Playing Nicely with Others in a Shared Environment________________________________________108
Chapter 6. Biological Research on the Web________________________________________120
6.1 Using Search Engines_________________________________________120
6.2 Finding Scientific Articles________________________________________122
6.3 The Public Biological Databases________________________________________126
6.4 Searching Biological Databases________________________________________131
6.5 Depositing Data into the Public Databases________________________________________138
6.6 Finding Software________________________________________138
6.7 Judging the Quality of Information________________________________________139
Chapter 7. Sequence Analysis, Pairwise Alignment, and Database Searching________________________142
7.1 Chemical Composition of Biomolecules________________________________________143
7.2 Composition of DNA and RNA________________________________________143
7.3 Watson and Crick Solve the Structure of DNA________________________________________144
7.4 Development of DNA Sequencing Methods________________________________________146
7.5 Genefinders and Feature Detection in DNA________________________________________149
7.6 DNA Translation________________________________________151
7.7 Pairwise Sequence Comparison________________________________________152
7.8 Sequence Queries Against Biological Databases________________________________________160
7.9 Multifunctional Tools for Sequence Analysis________________________________________167
Chapter 8. Multiple Sequence Alignments, Trees, and Profiles________________________________________169
8.1 The Morphological to the Molecular________________________________________169
8.2 Multiple Sequence Alignment________________________________________170
8.3 Phylogenetic Analysis________________________________________175
8.4 Profiles and Motifs________________________________________180
Chapter 9. Visualizing Protein Structures and Computing Structural Properties_________________189
9.1 A Word About Protein Structure Data________________________________________189
9.2 The Chemistry of Proteins________________________________________190
9.3 Web-Based Protein Structure Tools________________________________________201
9.4 Structure Visualization________________________________________202
9.5 Structure Classification________________________________________210
9.6 Structural Alignment________________________________________215
9.7 Structure Analysis________________________________________218
9.8 Solvent Accessibility and Interactions________________________________________221
9.9 Computing Physicochemical Properties________________________________________224
9.10 Structure Optimization________________________________________226
9.11 Protein Resource Databases________________________________________229
9.12 Putting It All Together________________________________________230
Chapter 10. Predicting Protein Structure and Function from Sequence___________________________232
10.1 Determining the Structures of Proteins________________________________________232
10.2 Predicting the Structures of Proteins________________________________________236
10.3 From 3D to 1D________________________________________237
10.4 Feature Detection in Protein Sequences________________________________________238
10.5 Secondary Structure Prediction________________________________________239
10.6 Predicting 3D Structure________________________________________243
10.7 Putting It All Together: A Protein Modeling Project________________________________________247
10.8 Summary________________________________________252
Chapter 11. Tools for Genomics and Proteomics________________________________________253
11.1 From Sequencing Genes to Sequencing Genomes________________________________________254
11.2 Sequence Assembly________________________________________258
11.3 Accessing Genome Informationon the Web________________________________________259
11.4 Annotating and Analyzing Whole Genome Sequences________________________________________263
11.5 Functional Genomics: New Data Analysis Challenges________________________________________265
11.6 Proteomics________________________________270
11.7 Biochemical Pathway Databases________________________________________274
11.8 Modeling Kinetics and Physiology________________________________________277
11.9 Summary________________________________________278
Chapter 12. Automating Data Analysis with Perl________________________________________280
12.1 Why Perl? ________________________________________280
12.2 Perl Basics________________________________________281
12.3 Pattern Matching and Regular Expressions________________________________________286
12.4 Parsing BLAST Output Using Perl________________________________________287
12.5 Applying Perl to Bioinformatics________________________________________292
Chapter 13. Building Biological Databases________________________________________296
13.1 Types of Databases________________________________________296
13.2 Database Software________________________________________303
13.3 Introduction to SQL________________________________________305
13.4 Installing the MySQL DBMS________________________________________310
13.5 Database Design________________________________________314
13.6 Developing WebBased Software That Interacts with Databases___________________________________317
Chapter 14. Visualization and Data Mining________________________________________324
14.1 Preparing Your Data________________________________________324
14.2 Viewing Graphics________________________________________325
14.3 Sequence Data Visualization________________________________________326
14.4 Networks and Pathway Visualization________________________________________328
14.5 Working with Numerical Data________________________________________329
14.6 Visualization: Summary________________________________________334
14.7 Data Mining and Biological Information________________________________________335
Biblio.1 Unix________________________________________340
Biblio.2 SysAdmin________________________________________340
Biblio.3 Perl________________________________________340
Biblio.4 General Reference________________________________________341
Biblio.5 Bioinformatics Reference________________________________________341
Biblio.6 Molecular Biology/Biology Reference________________________________________341
Biblio.7 Protein Structure and Biophysics________________________________________341
Biblio.8 Genomics________________________________________342
Biblio.9 Biotechnology________________________________________342
Biblio.10 Databases________________________________________342
Biblio.11 Visualization________________________________________342
Biblio.12 Data Mining________________________________________343
Colophon________________________________________344