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Computational Biology. A Hypertextbook. Edition No. 1. ASM Books

  • ID: 5225036
  • Book
  • January 2018
  • 210 Pages
  • John Wiley and Sons Ltd

An introduction to the world of bioinformatics

Massive increases in computing power and the ability to routinely sequence whole genomes of living organisms have begun to fundamentally alter our understanding of biology, medicine, and agriculture. At the intersection of the growing information and genomics revolutions sits bioinformatics, which uses modern computational power to reveal patterns in biological data sets, especially DNA, RNA, and protein sequences.

Computational Biology: A Hypertextbook, by Scott Kelley and Dennis Didulo, provides a wonderful introduction for anyone who wants to learn the basics of bioinformatics. This book is more than a textbook because of the wealth of online ancillary materials and how the print and electronic components are integrated to form a complete educational resource. Aspects that make Computational Biology: A Hypertextbook a unique and valuable tool for teaching and learning bioinformatics include

  • Clear explanations of the basic biology of DNA, RNA, and proteins and how the related bioinformatics algorithms work
  • Extensive exercises that enable students to practice with the same bioinformatics applications that are used by scientists worldwide
  • Tutorials, sample data sets, and interactive learning tools developed with teachers in mind and field-tested by hundreds of students
  • Online tutorials and curated web links that are accurate (instead of frustrating!) and won't lead to dead ends
  • Online resources that work on multiple platforms and electronic devices

Computational Biology: A Hypertextbook is written in an accessible voice, punctuated with humor, and designed to significantly increase computational competencies. Biology and computer science undergraduate and graduate students will thoroughly enjoy learning from this unique hypertextbook, as will anyone with an interest in exploring this burgeoning topic.

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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

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Scott T. Kelley
Dennis Didulo
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