Handbook of Computational Molecular Biology details the algorithms necessary to solve novel problems and manage the massive amounts of data housed in biological databases throughout the world.

Features:

• Presents the first comprehensive distillation of accumulated knowledge in computational biology
• Links each topic to applications in molecular biology while building on fundamental concepts
• Takes an algorithmic point of view for immediate implementation and easy reference
• Includes numerous illustrations to highlight the discussion as well as many references for more in-depth information

Contents

Sequence Alignments

• Pairwise Sequence Alignments
• Spliced Alignment and Similarity-Based Gene Recognition
• Multiple Sequence Alignment
• Parametric Sequence Alignment

String Data Structures

• Lookup Tables, Suffix Trees and Suffix Arrays
• Suffix Tree Applications in Computational Biology
• Enhanced Suffix Arrays and Applications

Genome Assembly and EST Clustering

• Computational Methods for Genome Assembly
• Assembling the Human Genome
• Comparative Methods for Sequence Assembly
• Information Theoretic Approach to Genome Reconstruction
• Expressed Sequence Tags: Clustering and Applications
• Algorithms for Large-Scale Clustering and Assembly of Biological Sequence Data

Genome-Scale Computational Methods

• Comparisons of Long Genomic Sequences: Algorithms and Applications
• Chaining Algorithms and Applications in Comparative Genomics
• Computational Analysis of Alternative Splicing
• Human Genetic Linkage Analysis
• Combinatorial Methods for Haplotype Inference

Phylogenetics

• An Overview of Phylogeny Reconstruction
• Consensus Trees and Supertrees
• Large-Scale Phylogenetic Analysis
• High-Performance Phylogeny Reconstruction

Microarrays and Gene Expression Analysis

• Microarray Data: Annotation, Storage, Retrieval and Communication
• Computational Methods for Microarray Design
• Clustering Algorithms for Gene Expression Analysis
• Biclustering Algorithms: A Survey
• Identifying Gene Regulatory Networks from Gene Expression Data
• Modeling and Analysis of Gene Networks Using Feedback Control Theory

Computational Structural Biology

• Predicting Protein Secondary and Supersecondary Structure
• Protein Structure Prediction with Lattice Models
• Protein Structure Determination via NMR Spectral Data
• Geometric Processing of Reconstructed 3D Maps of Molecular Complexes
• In Search of Remote Homolog
• Biomolecular Modeling using Parallel Supercomputers

Bioinformatic Databases and Data Mining

• String Search in External Memory: Data Structures and Algorithms
• Index Structures for Approximate Matching in Sequence Databases
• Algorithms for Motif Search
• Data Mining in Computational Biology

Index

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