part Part I: Sequence Alignments -- chapter 1 Pairwise Sequence Alignment -- chapter 2 Spliced Alignment and Similarity-based Gene Recognition -- chapter 3 Multiple Sequence Alignment -- chapter 4 Parametric Sequence Alignment -- part Part II: String Data Structures -- chapter 5 Lookup Tables, Suffix Trees and Suffix Arrays -- chapter 6 Suffix Tree Applications in Computational Biology -- chapter 7 Enhanced Suffix Arrays and Applications -- part Part III: Genome Assembly and EST Clustering -- chapter 8 Computational Methods for Genome Assembly -- chapter 9 Assembling the Human Genome -- chapter 10 Comparative Methods for Sequence Assembly -- chapter 11 Information Theoretic Approach to Genome Reconstruction -- chapter 12 Expressed Sequence Tags: Clustering and Applications -- chapter 13 Algorithms for Large-Scale Clustering and Assembly of Biological Sequence Data -- part Part IV: Genome-Scale Computational Methods -- chapter 14 Comparisons of Long Genomic Sequences: Algorithms and Applications -- chapter 15 Chaining Algorithms and Applications in Comparative Genomics -- chapter 16 Computational Analysis of Alternative Splicing -- chapter 17 Human Genetic Linkage Analysis -- chapter 18 Haplotype Inference -- part Part V: Phylogenetics -- chapter 19 An Overview of Phylogeny Reconstruction -- chapter 20 Consensus Trees and Supertrees -- chapter 21 Large-scale Phylogenetic Analysis -- chapter 22 High-Performance Algorithms for Phylogeny Reconstruction with Maximum Parsimony -- part Part VI: Microarrays and Gene Expression Analysis -- chapter 23 Microarray Data: Annotation, Storage, Retrieval and Communication -- chapter 24 Computational Methods for Microarray Design -- chapter 25 Clustering Algorithms for Gene Expression Analysis -- chapter 26 Biclustering Algorithms: A Survey -- chapter 27 Identifying Gene Regulatory Networks from Gene Expression Data -- chapter 28 Modeling and Analysis of Gene Networks Using Feedback Control Theory -- part Part VII: Computational Structural Biology -- chapter 29 Predicting Protein Secondary and Supersecondary Structure -- chapter 30 Protein Structure Prediction with Lattice Models -- chapter 31 Protein Structure Determination via NMR Spectral Data -- chapter 32 Geometric and Signal Processing of Reconstructed 3D Maps of Molecular Complexes -- chapter 33 In Search of Remote Homolog -- chapter 34 Biomolecular Modeling using Parallel Supercomputers -- part PartVIII: Bioinformatic Databases and Data Mining -- chapter 35 String Search in External Memory: Data Structures and Algorithms -- chapter 36 Index Structures for Approximate Matching in Sequence Databases -- chapter 37 Algorithms for Motif Search -- chapter 38 Data Mining in Computational Biology.