Introduction to Computational Biology

Preface Introduction Molecular Biology Mathematics, Statistics, and Computer Science Some Molecular Biology DNA and Proteins The Central Dogma The Genetic Code Transfer RNA and Protein Sequences Genes Are Not Simple Biological Chemistry Restriction Maps Introduction Graphs Interval Graphs Measuring Fragment Sizes Multiple Maps Double Digest Problem Classifying Multiple Solutions Algorithms for DDP Algorithms and Complexity DDP is N P-Complete Approaches to DDP Simulated Annealing: TSP and DDP Mapping with Real Data Cloning and Clone Libraries A Finite Number of Random Clones Libraries by Complete Digestion Libraries by Partial Digestion Genomes per Microgram Physical Genome Maps: Oceans, Islands, and Anchors Mapping by Fingerprinting Mapping by Anchoring An Overview of Clone Overlap Putting It Together Sequence Assembly Shotgun Sequencing Sequencing by Hybridization Shotgun Sequencing Revisited Databases and Rapid Sequence Analysis DNA and Protein Sequence Databases A Tree Representation of a Sequence Hashing a Sequence Repeats in a Sequence Sequence Comparison by Hashing Sequence Comparison with at most l Mismatches Sequence Comparison by Statistical Content Dynamic Programming Alignment of Two Sequences The Number of Alignments Shortest and Longest Paths in a Network Global Distance Alignment Global Similarity Alignment Fitting One Sequence into Another Local Alignment and Clumps Linear Space Algorithms Tracebacks Inversions Map Alignment Parametric Sequence Comparisons Multiple Sequence Alignment The Cystic Fibrosis Gene Dynamic Programming in r-Dimensions Weighted-Average Sequences Profile Analysis Alignment by Hidden Markov Models Consensus Word Analysis Probability and Statistics for Sequence Alignment Global Alignment Local Alignment Extreme Value Distributions The Chein-Stein Method Poisson Approximation and Long Matches Sequence Alignment with Scores Probability and Statistics for Sequence Patterns A Central Limit Theorem Nonoverlapping Pattern Counts Poisson Approximation Site Distributions RNA Secondary Structure Combinatorics Minimum Free-energy Structures Consensus folding Trees and Sequences Trees Distance Parsimony Maximum Likelihood Trees Sources and Perspectives Molecular Biology Physical Maps and Clone Libraries Sequence Assembly Sequence Comparisons Probability and Statistics RNA Secondary Structure Trees and Sequences References Problem Solutions and Hints Mathematical Notation Algorithm Index Author Index Subject Index