Developing Bioinformatics Computer Skills

Developing Bioinformatics Computer Skills

Part I: Introduction

Chapter 1. Biology in the Computer Age
  Section 1.1. How Is Computing Changing Biology?
  Section 1.2. Isn't Bioinformatics Just About Building Databases?
  Section 1.3. What Does Informatics Mean to Biologists?
  Section 1.4. What Challenges Does Biology Offer Computer Scientists?
  Section 1.5. What Skills Should a Bioinformatician Have?
  Section 1.6. Why Should Biologists Use Computers?
  Section 1.7. How Can I Configure a PC to Do Bioinformatics Research?
  Section 1.8. What Information and Software Are Available?
  Section 1.9. Can I Learn a Programming Language Without Classes?
  Section 1.10. How Can I Use Web Information?
  Section 1.11. How Do I Understand Sequence Alignment Data?
  Section 1.12. How Do I Write a Program to Align Two Biological Sequences?
  Section 1.13. How Do I Predict Protein Structure from Sequence?
  Section 1.14. What Questions Can Bioinformatics Answer?

Chapter 2. Computational Approaches to Biological Questions
  Section 2.1. Molecular Biology's Central Dogma
  Section 2.2. What Biologists Model
  Section 2.3. Why Biologists Model
  Section 2.4. Computational Methods Covered in This Book
  Section 2.5. A Computational Biology Experiment

Part II: The Bioinformatics Workstation

Chapter 3. Setting Up Your Workstation
  Section 3.1. Working on a Unix System
  Section 3.2. Setting Up a Linux Workstation
  Section 3.3. How to Get Software Working
  Section 3.4. What Software Is Needed?

Chapter 4. Files and Directories in Unix
  Section 4.1. Filesystem Basics
  Section 4.2. Commands for Working with Directories and Files
  Section 4.3. Working in a Multiuser Environment

Chapter 5. Working on a Unix System
  Section 5.1. The Unix Shell
  Section 5.2. Issuing Commands on a Unix System
  Section 5.3. Viewing and Editing Files
  Section 5.4. Transformations and Filters
  Section 5.5. File Statistics and Comparisons
  Section 5.6. The Language of Regular Expressions
  Section 5.7. Unix Shell Scripts
  Section 5.8. Communicating with Other Computers
  Section 5.9. Playing Nicely with Others in a Shared Environment

Part III: Tools for Bioinformatics

Chapter 6. Biological Research on the Web
  Section 6.1. Using Search Engines
  Section 6.2. Finding Scientific Articles
  Section 6.3. The Public Biological Databases
  Section 6.4. Searching Biological Databases
  Section 6.5. Depositing Data into the Public Databases
  Section 6.6. Finding Software
  Section 6.7. Judging the Quality of Information

Chapter 7. Sequence Analysis, Pairwise Alignment, and Database Searching
  Section 7.1. Chemical Composition of Biomolecules
  Section 7.2. Composition of DNA and RNA
  Section 7.3. Watson and Crick Solve the Structure of DNA
  Section 7.4. Development of DNA Sequencing Methods
  Section 7.5. Genefinders and Feature Detection in DNA
  Section 7.6. DNA Translation
  Section 7.7. Pairwise Sequence Comparison
  Section 7.8. Sequence Queries Against Biological Databases
  Section 7.9. Multifunctional Tools for Sequence Analysis

Chapter 8. Multiple Sequence Alignments, Trees, and Profiles
  Section 8.1. The Morphological to the Molecular
  Section 8.2. Multiple Sequence Alignment
  Section 8.3. Phylogenetic Analysis
  Section 8.4. Profiles and Motifs

Chapter 9. Visualizing Protein Structures and Computing Structural Properties
  Section 9.1. A Word About Protein Structure Data
  Section 9.2. The Chemistry of Proteins
  Section 9.3. Web-Based Protein Structure Tools
  Section 9.4. Structure Visualization
  Section 9.5. Structure Classification
  Section 9.6. Structural Alignment
  Section 9.7. Structure Analysis
  Section 9.8. Solvent Accessibility and Interactions
  Section 9.9. Computing Physicochemical Properties
  Section 9.10. Structure Optimization
  Section 9.11. Protein Resource Databases
  Section 9.12. Putting It All Together

Chapter 10. Predicting Protein Structure and Function from Sequence
  Section 10.1. Determining the Structures of Proteins
  Section 10.2. Predicting the Structures of Proteins
  Section 10.3. From 3D to 1D
  Section 10.4. Feature Detection in Protein Sequences
  Section 10.5. Secondary Structure Prediction
  Section 10.6. Predicting 3D Structure
  Section 10.7. Putting It All Together: A Protein Modeling Project
  Section 10.8. Summary

Chapter 11. Tools for Genomics and Proteomics
  Section 11.1. From Sequencing Genes to Sequencing Genomes
  Section 11.2. Sequence Assembly
  Section 11.3. Accessing Genome Informationon the Web
  Section 11.4. Annotating and Analyzing Whole Genome Sequences
  Section 11.5. Functional Genomics: New Data Analysis Challenges
  Section 11.6. Proteomics
  Section 11.7. Biochemical Pathway Databases
  Section 11.8. Modeling Kinetics and Physiology
  Section 11.9. Summary

Part IV: Databases and Visualization

Chapter 12. Automating Data Analysis with Perl
  Section 12.1. Why Perl?
  Section 12.2. Perl Basics
  Section 12.3. Pattern Matching and Regular Expressions
  Section 12.4. Parsing BLAST Output Using Perl
  Section 12.5. Applying Perl to Bioinformatics

Chapter 13. Building Biological Databases
  Section 13.1. Types of Databases
  Section 13.2. Database Software
  Section 13.3. Introduction to SQL
  Section 13.4. Installing the MySQL DBMS
  Section 13.5. Database Design
  Section 13.6. Developing Web-Based Software That Interacts with Databases

Chapter 14. Visualization and Data Mining
  Section 14.1. Preparing Your Data
  Section 14.2. Viewing Graphics
  Section 14.3. Sequence Data Visualization
  Section 14.4. Networks and Pathway Visualization
  Section 14.5. Working with Numerical Data
  Section 14.6. Visualization: Summary
  Section 14.7. Data Mining and Biological Information

Bibliography
  Section Biblio.1. Unix
  Section Biblio.2. SysAdmin
  Section Biblio.3. Perl
  Section Biblio.4. General Reference
  Section Biblio.5. Bioinformatics Reference
  Section Biblio.6. Molecular Biology/Biology Reference
  Section Biblio.7. Protein Structure and Biophysics
  Section Biblio.8. Genomics
  Section Biblio.9. Biotechnology
  Section Biblio.10. Databases
  Section Biblio.11. Visualization
  Section Biblio.12. Data Mining

Structure of This Book

We've arranged the material in this book to allow you to read it from start to finish or to skip around, digesting later sections before previous ones. It's divided into four parts:

Part I

Chapter 1 defines bioinformatics as a discipline, delves into a bit of history, and provides a brief tour of what the book covers and why.

Chapter 2 introduces the core concepts of bioinformatics and molecular biology and the technologies and research initiatives that have made increasing amounts of biological data available. It also covers the ever-growing list of basic computer procedures every biologist should know.

Part II

Chapter 3 introduces Unix, then moves on to the basics of installing Linux on a PC and getting software up and running.

Chapter 4 covers the ins and outs of moving around a Unix filesystem, including file hierarchies, naming schemes, commonly used directory commands, and working in a multiuser environment.

Chapter 5 explains many Unix commands users will encounter on a daily basis, including commands for viewing, editing, and extracting information from files; regular expressions; shell scripts; and communicating with other computers.

Part III

Chapter 6 is about the art of finding biological information on the Web. The chapter covers search engines and searching, where to find scientific articles and software, how to use the online information sources, and the public biological databases.

Chapter 7 begins with a review of molecular evolution and then moves on to cover the basics of pairwise sequence-analysis techniques such as predicting gene location, global and local alignment, and local alignment-based searching against databases using BLAST and FASTA. The chapter concludes with coverage of multifunctional tools for sequence analysis.

Chapter 8 moves on to study groups of related genes or proteins. It covers strategies for multiple sequence alignment with tools such as ClustalW and Jalview, then discusses tools for phylogenetic analysis, and constructing profiles and motifs.

Chapter 9 covers 3D analysis of proteins and the tools used to compute their structural properties. The chapter begins with a review of protein chemistry and quickly moves to a discussion of web-based protein structure tools; structure classification, alignment, and analysis; solvent accessibility and solvent interactions; and computing physicochemical properties of proteins. The chapter concludes with structure optimization and a tour through protein resource databases.

Chapter 10 covers the tools that determine the structures of proteins from their sequences. The chapter discusses feature detection in protein sequences, secondary structure prediction, predicting 3D structure. It concludes with an example project in protein modeling.

Chapter 11 puts it all together. Up to now we've covered tools and techniques for analyzing single sequences or structures, and for comparing multiple sequences of single-gene length. This chapter discusses some of the datatypes and tools that are becoming available for studying the integrated function of all the genes in a genome, including sequencing an entire genome, accessing genome information on the Web, annotating and analyzing whole genome sequences, and emerging technologies and proteomics.

Part IV

Chapter 12 shows you how a programming language such as Perl can help you sift through mountains of data to extract just the information you require. It won't teach you to program in Perl, but the chapter gives you a brief introduction to the language and includes examples to start you on your way toward learning to program.

Chapter 13 is an introduction to database concepts. It covers the types of databases used in biological research, the database software that builds them, database languages (in particular, the SQL language), and developing web-based software that interacts with databases.

Chapter 14 covers the computational tools and techniques that allow you to make sense of your results. The first part of the chapter introduces programs that are used to visualize data arising from bioinformatics research. They range from general-purpose plotting and statistical packages for numerical data, such as Grace and gnuplot, to programs such as TEXshade that are dedicated to presenting sequence and structural information in an interpretable form. The second part of the chapter presents tools for data mining—the process of finding, interpreting, and evaluating patterns in large sets of data—in the context of applications in bioinformatics.