Developing Bioinformatics Computer Skills

Preface

I: Introduction

1: Biology in the Computer Age

How Is Computing Changing Biology?

Isn't Bioinformatics Just About Building Databases?

What Does Informatics Mean to Biologists?

What Challenges Does Biology Offer Computer Scientists?

What Skills Should a Bioinformatician Have?

Why Should Biologists Use Computers?

How Can I Configure a PC to Do Bioinformatics Research?

What Information and Software Are Available?

Can I Learn a Programming Language Without Classes?

How Can I Use Web Information?

How Do I Understand Sequence Alignment Data?

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

How Do I Predict Protein Structure from Sequence?

What Questions Can Bioinformatics Answer?

2: Computational Approaches to Biological Questions

Molecular Biology's Central Dogma

What Biologists Model

Why Biologists Model

Computational Methods Covered in This Book

A Computational Biology Experiment

II: The Bioinformatics Workstation

3: Setting Up Your Workstation

Working on a Unix system

Setting Up a Linux Workstation

How to Get Software Working

What Software Is Needed?

4: Files and Directories in Unix

Filesystem Basics

Commands for Working with Directories and Files

Working in a Multiuser Environment

5: Working on a Unix System

The Unix Shell

Issuing Commands on a Unix System

Viewing andEditing Files

Transformations and Filters

File Statistics and Comparisons

The Language of Regular Expressions

Unix Shell Scripts

Communicating with Other Computers

Playing Nicely with Others in a Shared Environment

III: Tools for Bioinformatics

6: Biological Research on the Web

Using Search Engines

Finding Scientific Articles

The Public Biological Databases

Searching Biological Databases

Depositing Data into the Public Databases

Finding Software

Judging the Quality of Information

7: Sequence Analysis, Pairwise Alignment, and Database Searching

Chemical Composition of Biomolecules

Composition of DNA and RNA

Watson and Crick Solve the Structure of DNA

Development of DNA Sequencing Methods

Genefinders and Feature Detection in DNA

DNA Translation

Pairwise Sequence Comparison

Sequence Queries Against Biological Databases

Multifunctional Tools for Sequence Analysis

8: Multiple Sequence Alignments, Trees, and Profiles

The Morphological to the Molecular

Multiple Sequence Alignment

Phylogenetic Analysis

Profiles and Motifs

9: Visualizing Protein Structures and Computing Structural Properties

A Word About Protein Structure Data

The Chemistry of Proteins

Web-Based Protein Structure Tools

Structure Visualization

Structure Classification

Structural Alignment

Structure Analysis

Solvent Accessibility and Interactions

Computing Physicochemical Properties

Structure Optimization

Protein Resource Databases

Putting It All Together

10: Predicting Protein Structure and Function from Sequence

Determining the Structures of Proteins

Predicting the Structures of Proteins

From 3D to 1D

Feature Detection in Protein Sequences

Secondary Structure Prediction

Predicting 3D Structure

Putting It All Together: A Protein Modeling Project

Summary

11: Tools for Genomics and Proteomics

From Sequencing Genes to Sequencing Genomes

Sequence Assembly

Accessing Genome Informationon the Web

Annotating and Analyzing Whole Genome Sequences

Functional Genomics: New Data Analysis Challenges

Proteomics

Biochemical Pathway Databases

Modeling Kinetics and Physiology

Summary

IV: Databases and Visualization

12: Automating Data Analysis with Perl

Why Perl?

Perl Basics

Pattern Matching and Regular Expressions

Parsing BLAST Output Using Perl

Applying Perl to Bioinformatics

13: Building Biological Databases

Types of Databases

Database Software

Introduction to SQL

Installing the MySQL DBMS

Database Design

Developing Web-Based Software That Interacts with Databases

14: Visualization and Data Mining

Preparing Your Data

Viewing Graphics

Sequence Data Visualization

Networks and Pathway Visualization

Bibliography

Index