Developing Bioinformatics Computer Skills

Developing Bioinformatics Computer Skills is for scientists and students who are learning computational approaches to biology for the first time, as well as for experienced biology researchers who are just starting to use computers to handle their data. 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, and data visualization.

Written in a clear, engaging style, Developing Bioinformatics Computer Skills will help biologists develop a structured approach to biological data as well as the tools they'll need to analyze the data.

Contents

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