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Bioinformatics Algorithms.pdf

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Cover
Overview
Contents
List of Code Challenges
About the Textbook
Chapter 1: Where in the Genome Does DNA Replication Begin?
Chapter 2: Which DNA Patterns Play the Role of Molecular Clocks?
Chapter 3: How Do We Assemble Genomes?
Chapter 4: How Do We Sequence Antibiotics?
Chapter 5: How Do We Compare DNA Sequences?
Chapter 6: Are There Fragile Regions in the Human Genome?
Bibliography
Image Courtesies
Welcome! Thank you for joining us! As you explore this book, you will find a number of active learning components that help you learn the material at your own pace. 1. CODE CHALLENGES ask you to implement the algorithms that you will en- counter (in any programming language you like). These code challenges are hosted in the “Bioinformatics Textbook Track” location on Rosalind (http:// rosalind.info), a website that will automatically test your implementations. 2. CHARGING STATIONS provide additional insights on implementing the algo- rithms you encounter. However, we suggest trying to solve a Code Challenge before you visit a Charging Station. 3. EXERCISE BREAKS offer “just in time” assessments testing your understanding of a topic before moving to the next one. 4. STOP and Think questions invite you to slow down and contemplate the current material before continuing to the next topic. 5. DETOURS provide extra content that didn’t quite fit in the main text. DETOUR DETOUR 6. FINAL CHALLENGES ask you to apply what you have learned to real experi- mental datasets. This textbook powers our popular online courses on Coursera. We encourage you to sign up for a session and learn this material while interacting with thousands of other talented students from around the world. You can also find lecture videos and PowerPoint slides at the textbook website, http://bioinformaticsalgorithms.org. i
Bioinformatics Algorithms:An Active Learning Approach2nd Edition, Vol. IPhillip Compeau & Pavel Pevznerhttp://bioinformaticsalgorithms.org© 2015
Copyright © 2015 by Phillip Compeau and Pavel Pevzner. All rights reserved. This book or any portion thereof may not be reproduced or used in any manner whatso- ever without the express written permission of the publisher except for the use of brief quotations in a book review. Printed in the United States of America First Printing, 2015 ISBN: 978-0-9903746-1-9 Library of Congress Control Number: 2015945208 Active Learning Publishers, LLC 9768 Claiborne Square La Jolla, CA 92037
To my family. — P. C. To my parents. — P. P.
Volume I Overview CHAPTER 1 — p. 2 CHAPTER 2 — p. 66 vi
CHAPTER 3 — p. 115 CHAPTER 4 — p. 182 CHAPTER 5 — p. 222 CHAPTER 6 — p. 292 vii
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