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Ever since the structure of DNA was unraveled in 1953, molecular biology has witnessed tremendous advances. With the increase in our ability to manipulate biomolecular sequences, a huge amount of data has been and is being generated. The need to process the information that is pouring from laboratories all over the world, so that it can be of use to further scientific advance, has created entirely new problems that are interdisciplinary in nature. Scientists from the biological sciences are the creators and ultimate users of this data. However, due to sheer size and complexity, between creation and use the help of many other diisciplines is required, in particular those from the mathematical and computing sciences. This need has created a new field, which goes by the general name of computational molecular biology.

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