Cover -- Half-title -- Title -- Copyright -- Dedication -- Contents -- Preface -- Acknowledgments -- CHAPTER ONE The Central Dogma -- 1.1 DNA and RNA -- 1.2 Chromosomes -- 1.3 Proteins -- 1.4 The Central Dogma -- 1.5 Transcription and Translation in Perl -- 1.6 Exercise -- 1.7 Complete Program Listings -- 1.8 Bibliographic Notes -- CHAPTER TWO RNA Secondary Structure -- 2.1 Messenger and Catalytic RNA -- 2.2 Levels of RNA Structure -- 2.3 Constraints on Secondary Structure -- 2.4 RNA Secondary Structures in Perl -- 2.4.1 Counting Hydrogen Bonds -- 2.4.2 Folding RNA -- 2.5 Exercises -- 2.6 Complete Program Listings -- 2.7 Bibliographic Notes -- CHAPTER THREE Comparing DNA Sequences -- 3.1 DNA Sequencing and Sequence Assembly -- 3.2 Alignments and Similarity -- 3.3 Alignment and Similarity in Perl -- 3.4 Exercises -- 3.5 Complete Program Listings -- 3.6 Bibliographic Notes -- CHAPTER FOUR Predicting Species: Statistical Models -- 4.1 Perl Subroutine Libraries -- 4.2 Species Prediction in Perl -- 4.3 Exercises -- 4.4 Complete Program Listings -- 4.5 Bibliographic Note -- CHAPTER FIVE Substitution Matrices for Amino Acids -- 5.1 More on Homology -- 5.2 Deriving Substitution Matrices from Alignments -- 5.3 Substitution Matrices in Perl -- 5.4 The PAM Matrices -- 5.5 PAM Matrices in Perl -- 5.6 Exercises -- 5.7 Complete Program Listings -- 5.8 Bibliographic Notes -- CHAPTER SIX Sequence Databases -- 6.1 FASTA Format -- 6.2 GenBank Format -- 6.3 GenBank's Feature Locations -- 6.4 Reading Sequence Files in Perl -- 6.4.1 Object-Oriented Programming in Perl -- 6.4.2 The SimpleReader Class -- 6.4.3 Hiding File Formats with Method Inheritance -- 6.5 Exercises -- 6.6 Complete Program Listings -- 6.7 Bibliographic Notes -- CHAPTER SEVEN Local Alignment and the BLAST Heuristic -- 7.1 The Smith-Waterman Algorithm -- 7.2 The BLAST Heuristic.

7.2.1 Preprocessing the Query String -- 7.2.2 Scanning the Target String -- 7.3 Implementing BLAST in Perl -- 7.4 Exercises -- 7.5 Complete Program Listings -- 7.6 Bibliographic Notes -- CHAPTER EIGHT Statistics of BLAST Database Searches -- 8.1 BLAST Scores for Random DNA -- 8.2 BLAST Scores for Random Residues -- 8.3 BLAST Statistics in Perl -- 8.4 Interpreting BLAST Output -- 8.5 Exercise -- 8.6 Complete Program Listings -- 8.7 Bibliographic Notes -- CHAPTER NINE Multiple Sequence Alignment I -- 9.1 Extending the Needleman-Wunsch Algorithm -- 9.2 NP-Completeness -- 9.3 Alignment Merging: A Building Block for Heuristics -- 9.4 Merging Alignments in Perl -- 9.5 Finding a Good Merge Order -- 9.6 Exercises -- 9.7 Complete Program Listings -- 9.8 Bibliographic Notes -- CHAPTER TEN Multiple Sequence Alignment II -- 10.1 Pushing through the Matrix by Layers -- 10.2 Tunnel Alignments -- 10.3 A Branch-and-Bound Method -- 10.4 The Branch-and-Bound Method in Perl -- 10.5 Exercises -- 10.6 Complete Program Listings -- 10.7 Bibliographic Notes -- CHAPTER ELEVEN Phylogeny Reconstruction -- 11.1 Parsimonious Phylogenies -- 11.2 Assigning Sequences to Branch Nodes -- 11.3 Pruning the Trees -- 11.4 Implementing Phylogenies in Perl -- 11.5 Building the Trees in Perl -- 11.6 Exercise -- 11.7 Complete Program Listings -- 11.8 Bibliographic Notes -- CHAPTER TWELVE Protein Motifs and PROSITE -- 12.1 The PROSITE Database Format -- 12.2 Patterns in PROSITE and Perl -- 12.3 Suffix Trees -- 12.3.1 Suffix Links -- 12.3.2 The Efficiency of Adding -- 12.4 Suffix Trees for PROSITE Searching -- 12.5 Exercises -- 12.6 Complete Program Listings -- 12.7 Bibliographic Notes -- CHAPTER THIRTEEN Fragment Assembly -- 13.1 Shortest Common Superstrings -- 13.2 Practical Issues and the PHRAP Program -- 13.3 Reading Inputs for Assembly -- 13.4 Aligning Reads -- 13.5 Adjusting Qualities.

13.6 Assigning Reads to Contigs -- 13.7 Developing Consensus Sequences -- 13.8 Exercises -- 13.9 Complete Program Listings -- 13.10 Bibliographic Notes -- CHAPTER FOURTEEN Coding Sequence Prediction with Dicodons -- 14.1 A Simple Trigram Model -- 14.2 A Hexagram Model -- 14.3 Predicting All Genes -- 14.4 Gene Finding in Perl -- 14.5 Exercises -- 14.6 Complete Program Listings -- 14.7 Bibliographic Notes -- CHAPTER FIFTEEN Satellite Identification -- 15.1 Finding Satellites Efficiently -- 15.1.1 Suffix Testing -- 15.1.2 Satellite Testing -- 15.2 Finding Satellites in Perl -- 15.3 Exercises -- 15.4 Complete Program Listings -- 15.5 Bibliographic Notes -- CHAPTER SIXTEEN Restriction Mapping -- 16.1 A Backtracking Algorithm for Partial Digests -- 16.2 Partial Digests in Perl -- 16.3 Uncertain Measurement and Interval Arithmetic -- 16.3.1 Backtracking with Intervals -- 16.3.2 Interval Arithmetic in Perl -- 16.3.3 Partial Digests with Uncertainty in Perl -- 16.3.4 A Final Check for Interval Consistency -- 16.4 Exercises -- 16.5 Complete Program Listings -- 16.6 Bibliographic Notes -- CHAPTER SEVENTEEN Rearranging Genomes: Gates and Hurdles -- 17.1 Sorting by Reversals -- 17.2 Making a Wish List -- 17.3 Analyzing the Interaction Relation -- 17.4 Clearing the Hurdles -- 17.5 Happy Cliques -- 17.6 Sorting by Reversals in Perl -- 17.7 Exercise -- 17.8 Appendix: Correctness of Choice of Wish from Happy Clique -- 17.9 Complete Program Listings -- 17.10 Bibliographic Notes -- APPENDIX A Drawing RNA Cloverleaves -- A.1 Exercises -- A.2 Complete Program Listings -- A.3 Bibliographic Notes -- APPENDIX B Space-Saving Strategies for Alignment -- B.1 Finding Similarity Scores Compactly -- B.2 Finding Alignments Compactly -- B.3 Exercises -- B.4 Complete Program Listings -- B.5 Bibliographic Note -- APPENDIX C A Data Structure for Disjoint Sets -- C.1 Union by Rank.

C.2 Path Compression -- C.3 Complete Program Listings -- C.4 Bibliographic Note -- APPENDIX D Suggestions for Further Reading -- Bibliography -- Index.