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| Preface Book Overview Exercises Errors Acknowledgments 1 Basic Concepts of Molecular Biology 1.1 Life 1.2 Proteins 1.3 Nucleic Acids 1.3.1 DNA 1.3.2 RNA 1.4 The Mechanisms of Molecular Genetics 1.4.1 Genes and the Genetic Code 1.4.2 Transcription， Translation， and Protein Synthesis 1.4.3 Junk DNA and Reading Frames 1.4.4 Chromosomes 1.4.5 Is the Genome like a Computer Program? 1.5 How the Genome Is Studied 1.5.1 Maps and Sequences 1.5.2 Specific Techniques 1.6 The Human Genome Project 1.7 Sequence Databases Exercises Bibliographic Notes 2 Strings,Graphs,and Algorithms 2.1 Strings 2.2 Graphs 2.3 Algorithms Exercises Bibliographic Notes Sequence Comparison and Database Search 3.1 Biological Background 3.2 Comparing Two Sequences 3.2.1 Global Comparison-The Basic Algorithm 3.2.2 Local Comparison 3.2.3 Semiglobal Comparison 3.3 Extensions to the Basic Algorithms 3.3.1 Saving Space 3.3.2 General Gap Penalty Functions 3.3.3 Affine Gap Penalty Functions 3.3.4 Comparing Similar Sequences 3.4 Comparing Multiple Sequences 3.4.1 The SP Measure 3.4.2 Star Alignments 3.4.3 Tree Alignments 3.5 Database Search 3.5.1 PAM Matrices 3.5.2 BLAST 3.5.3 FAST 3.6 Other Issues 3.6.1 Similarity and Distance 3.6.2 Parameter Choice in Sequence Comparison 3.6.3 String Matching and Exact Sequence Comparison Summary Exercises Bibliographic Notes Fragment Assembly of DNA 4.1 Biological Background 4.1.1 The Ideal Case 4.t.2 Complications 4.1.3 Alternative Methods for DNA Sequencing 4.2 Models 4.2.1 Shortest Common Superstring 4.2.2 Reconstruction 4.2.3 Multicontig 4.3 Algorithms 4.3.1 Representing Overlaps 4.3.2 Paths Originating Superstrings 4.3.3 Shortest Superstrings as Paths 4.3.4 The Greedy Algorithm 4.3.5 Acyclic Subgraphs 4.4 Heuristics 4.4.1 Finding Overlaps …… 5 Physical Mapping of DNA 6 Phylogenetic Trees 7 Genome Rearrangements 8 Molecular Structure Prediction 9 Epilogue:Computing with DNA Answers to Selected References Index |
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