Developing Bioinformatics Computer Skills will help biologists, researchers, and students develop a structured approach to biological data and the computer tools they'll need to analyze it. The book covers the Unix file system, building tools and databases for bioinformatics, computational approaches to biological problems, an introduction to Perl for bioinformatics, data mining, data visualization, and tips for tailoring data analysis software to individual research needs.

Cynthia Gibas
Cynthia Gibas is an assistant professor of biology at Virginia Tech, in Blacksburg, Virginia. She's been a computational biologist since before computational biology was cool, and is currently learning to drive her spankin' new home-built Linux cluster. Her research interests include the structure and evolution of genomes, the properties of protein surfaces and interfaces, and prediction of protein structure. She teaches introductory courses in bioinformatics methods for biologists and is looking forward to her next real vacation, sometime in 2006.
Per Jambeck
Per Jambeck is a Ph.D. student in the bioengineering department at the University of California, San Diego. He has worked on computational biology problems since 1994, concentrating on machine learning applications in understanding multidimensional biological data. Per smiles wistfully at the mention of free time, but he manages to host shows at community and student-run radio stations anyway.

Preface

ix

I. Introduction

1

(44)

Biology in the Computer Age

3

(19)

How Is Computing Changing Biology?

4

(4)

Isn't Bioinformatics Just About Building Databases?

8

(4)

What Does Informatics Mean to Biologists?

12

(1)

What Challenges Does Biology Offer Computer Scientists?

13

(1)

What Skills Should a Bioinformatician Have?

13

(1)

Why Should Biologists Use Computers?

14

(2)

How Can I Configure a PC to Do Bioinformatics Research?

16

(2)

What Information and Software Are Available?

18

(1)

Can I Learn a Programming Language Without Classes?

18

(1)

How Can I Use Web Information?

19

(1)

How Do I Understand Sequence Alignment Data?

20

(1)

How Do I Write a Program to Align Two Biological Sequences?

20

(1)

How Do I Predict Protein Structure from Sequence?

21

(1)

What Questions Can Bioinformatics Answer?

21

(1)

Computational Approaches to Biological Questions

22

(23)

Molecular Biology's Central Dogma

22

(5)

What Biologists Model

27

(4)

Why Biologists Model

31

(1)

Computational Methods Covered in This Book

32

(6)

A Computational Biology Experiment

38

(7)

II. The Bioinformatics Workstation

45

(86)

Setting Up Your Workstation

47

(17)

Working on a Unix System

47

(3)

Setting Up a Linux Workstation

50

(6)

How to Get Software Working

56

(6)

What Software Is Needed?

62

(2)

Files and Directories in Unix

64

(23)

Filesystem Basics

64

(7)

Commands for Working with Directories and Files

71

(8)

Working in a Multiuser Environment

79

(8)

Working on a Unix System

87

(44)

The Unix Shell

87

(2)

Issuing Commands on a Unix System

89

(5)

Viewing and Editing Files

94

(7)

Transformations and Filters

101

(7)

File Statistics and Comparisons

108

(2)

The Language of Regular Expressions

110

(3)

Unix Shell Scripts

113

(1)

Communicating with Other Computers

114

(5)

Playing Nicely with Others in a Shared Environment

119

(12)

III. Tools for Bioinformatics

131

(198)

Biological Research on the Web

133

(26)

Using Search Engines

134

(2)

Finding Scientific Articles

136

(4)

The Public Biological Databases

140

(7)

Searching Biological Databases

147

(8)

Depositing Data into the Public Databases

155

(1)

Finding Software

155

(1)

Judging the Quality of Information

156

(3)

Sequence Analysis, Pairwise Alignment, and Database Searching

159

(32)

Chemical Composition of Biomolecules

160

(1)

Composition of DNA and RNA

161

(1)

Watson and Crick Solve the Structure of DNA

161

(3)

Development of DNA Sequencing Methods

164

(5)

Genefinders and Feature Detection in DNA

169

(2)

DNA Translation

171

(1)

Pairwise Sequence Comparison

172

(10)

Sequence Queries Against Biological Databases

182

(6)

Multifunctional Tools for Sequence Analysis

188

(3)

Multiple Sequence Alignments, Trees, and Profiles

191

(24)

The Morphological to the Molecular

191

(2)

Multiple Sequence Alignment

193

(6)

Phylogenetic Analysis

199

(6)

Profiles and Motifs

205

(10)

Visualizing Protein Structures and Computing Structural Properties

215

(53)

A Word About Protein Structure Data

216

(1)

The Chemistry of Proteins

217

(12)

Web-Based Protein Structure Tools

229

(2)

Structure Visualization

231

(10)

Structure Classification

241

(5)

Structural Alignment

246

(4)

Structure Analysis

250

(4)

Solvent Accessibility and Interactions

254

(4)

Computing Physicochemical Properties

258

(2)

Structure Optimization

260

(3)

Protein Resource Databases

263

(2)

Putting It All Together

265

(3)

Predicting Protein Structure and Function from Sequence

268

(26)

Determining the Structures of Proteins

269

(4)

Predicting the Structures of Proteins

273

(2)

From 3D to 1D

275

(1)

Feature Detection in Protein Sequences

276

(1)

Secondary Structure Prediction

277

(6)

Predicting 3D Structure

283

(4)

Putting It All Together: A Protein Modeling Project

287

(6)

Summary

293

(1)

Tools for Genomics and Proteomics

294

(35)

From Sequencing Genes to Sequencing Genomes

296

(5)

Sequence Assembly

301

(2)

Accessing Genome Information the Web

303

(4)

Annotating and Analyzing Whole Genome Sequences

307

(3)

Functional Genomics: New Data Analysis Challenges

310

(7)

Proteomics

317

(4)

Biochemical Pathway Databases

321

(4)

Modeling Kinetics and Physiology

325

(2)

Summary

327

(2)

IV. Databases and Visualization

329

(74)

Automating Data Analysis with Perl

331

(19)

Why Perl?

331

(1)

Perl Basics

332

(7)

Pattern Matching and Regular Expressions

339

(1)

Parsing BLAST Output Using Perl

340

(5)

Applying Perl to Bioinformatics

345

(5)

Building Biological Databases

350

(33)

Types of Databases

351

(8)

Database Software

359

(2)

Introduction to SQL

361

(5)

Installing the MySQL DBMS

366

(5)

Database Design

371

(4)

Developing Web-Based Software That Interacts with Databases

375

(8)

Visualization and Data Mining

383

(20)

Preparing Your Data

384

(1)

Viewing Graphics

385

(1)

Sequence Data Visualization

386

(2)

Networks and Pathway Visualization

388

(2)

Working with Numerical Data

390

(6)

Visualization: Summary

396

(1)

Data Mining and Biological Information

397

(6)

Bibliography

403

(6)

Index

409

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