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Table of Contents Preface Chapter One: Text 1 Introduction: Explorations and Indexes Box 1.1 The Fine Print Box 1.2 Finding words and motifs with your word processor follows pg 20 Box 1.3 Annotating Sequences by Hand follows pg 20 Chapter Two: Text 2 Essential First Steps Box 2.1 Two Reasons to Skip this Chapter follows pg 23 Box 2.2 Using this Chapter to Forge a New Relationship follows pg 23 Chapter Three: Text 3 Playing with DNA Sequences (and words) Using Regular Expressions Box 3.1 The Perl Community follows section1 on page 28 Box 3.2 What is the best language? follows section 2 on page 33 Box 3.3 Larry Wall's Rambling List of Suggestions follows section3 on page37 Box 3.4 Why do computer scientists count from zero? follows section5 on page 51 Chapter Four: Text 4 Your First Perl Programs with a Focus on String Analysis Box 4.1 Why repeats are interesting follows section 1 on page 63 Box 4.2 Alice Kober Linear B, Motif Frequencies follows section3 on page 65 Chapter Five: Text 5 Using Perl to Do Calculations Box 5.1 Napkin Math follows section 1 on page 104 Box 5.2 A Bookshelf of DNA follows section2 on page 108 Box 5.3 The Library of Babel follows section 3 on page 111 Box 5.4 Joining the Programming Community or Creating Your Own Version of It follows section 3 on page 111 Chapter Six: Text 6 Making Decisions Over and Over Again with Perl¿s ¿if¿ and ¿while¿ Box 6.1 Endless Loops and How to Stop Them follows section 7on page 130 Box 6.2 Eric Davidson follows section8 on page 140 Chapter Seven: Text 7 Subroutines Box 7.1 Erwin Chargaff follows section1 on page 144 Box 7.2 The Etymology of ¿Foobar follows section 2 on page 150 Box 7.3 Perl Poetry follows section3 on page 154 Box 7.4 More Tim Toady follows section 4 on page 155 Chapter Eight: Text Accessing Files of Sequences from Databases Box 8.1 Ten ways to look at DNA follows section 3 on page 178 Chapter Nine: Text 9 Arrays Box 9.1 Favorite Gene follows section 5 on page 192 Chapter Ten: Text 10 Hash Tables Box 10.1 The convoluted etymology and use of ¿octothorpe¿ and its many synonyms follows section 1 on page 221 Box 10.2 Chargaffian Clues follows section 2 on page 222 Box 10.3 Complexity--2X vs. X squared follows section 4 on page 230 Box 10.4 ¿The Three Bears¿ vs. ¿ follows section 5 on page 233 Chapter Eleven: Text 11 Phrasing Questions by Writing Algorithms Box 11.1 An Algorithm for Discovery follows section 1 on page 243 Box 11.2 Beauty I follows section 2 on page 246 Box 11.3 Importance of Beauty II follows section3 on page 248 Box 11.4 Speed I follows section 4 on page 249 Box 11.5 Speed II follows section5 on page 252 Box 11.6 Talking to Programmers follows section 6 on page 253 Chapter Twelve: Text 12 Regular Expressions Revisited Box 12.1 Go Ahead and Name it follows section 1 on page 257 Box 12.2 Hieroglyphics follows section2 on page 260 Box 12.3 Braille, the Skytale Code follows section3 on page 262 Chapter Thirteen: Text 13 Understanding Randomness Box 13.1 Ground Truth follows section1 on page 273 Box 13.2 DNA binding as a fuzzy¿ follows section2 on page 277 Box 13.3 Make your own DNA die. follows section 3 on page 278 Chapter Fourteen: Text 14 Modules Box 14.1 What about Bioperl? follows section 1 on page 287 Box 14.2 Fonts for DNA follows section 2 on page 289 Box 14.3 Musical DNA follows section 3 on page 294 Chapter Fifteen: Text 15 Conclusions Appendix I Appendix II Bibliography
Library of Congress Subject Headings for this publication:
Nucleotide sequence -- Data processing.
Amino acid sequence -- Data processing.
Perl (Computer program language).