This textbook is for anyone who needs to learn the basics of bioinformatics - the use of computational methods to better understand biological systems. Computational Biology covers the principles and applications of the computational methods used to study DNA, RNA, and proteins, including using biological databases such as NCBI and UniProt; performing BLAST, sequence alignments, and structural predictions; and creating phylogenetic trees. It includes a primer that can be used as a jumping off point for learning computer programming for bioinformatics.
This text can be used as a self-study guide, as a course focused on computational methods in biology/bioinformatics, or to supplement general courses that touch on topics included within the book. Computational Biology's robust interactive online components “gamify” the study of bioinformatics, allowing the reader to practice randomly generated problems on their own time to build confidence and skill and gain practical real-world experience. The online component also assures that the content being taught is up to date and accurately reflects the ever-changing landscape of bioinformatics web-based programs.
Table of Contents
Preface ix
For the Instructor xi
For the Student xiii
Acknowledgments xiv
About the Authors xv
Chapter –1 Getting Started 1
Chapter 00 Introduction 5
Activity 0.1: Biological Databases and Data Storage 20
Chapter 01 BLAST 31
Activity 1.1: BLAST Algorithm 36
Chapter 02 Protein Analysis 47
Activity 2.1: Hydrophobicity Plotting 52
Activity 2.2: Protein Secondary Structure Prediction 58
Chapter 03 Sequence Alignment 67
Activity 3.1: Dynamic Programming 74
Chapter 04 Patterns in the Data 91
Activity 4.1: Protein Sequence Motifs 94
Activity 4.2: Position-Specific Weight Matrices 102
Chapter 05 RNA Structure Prediction 111
Activity 5.1: RNA Structure Prediction 118
Chapter 06 Phylogenetics 133
Activity 6.1: Phylogenetic Analysis 140
Chapter 07 Probability: All Mutations are not Equal (-ly Probable) 157
Activity 7.1: Generating PAM and BLOSUM Substitution Matrices 163
Chapter 08 Bioinformatics Programming: A Primer 179
Index 191
