1st Edition

Introduction to Computational Biology Maps, Sequences and Genomes

By Michael S. Waterman Copyright 1995
    448 Pages
    by Chapman & Hall

    Biology is in the midst of a era yielding many significant discoveries and promising many more. Unique to this era is the exponential growth in the size of information-packed databases. Inspired by a pressing need to analyze that data, Introduction to Computational Biology explores a new area of expertise that emerged from this fertile field- the combination of biological and information sciences.

    This introduction describes the mathematical structure of biological data, especially from sequences and chromosomes. After a brief survey of molecular biology, it studies restriction maps of DNA, rough landmark maps of the underlying sequences, and clones and clone maps. It examines problems associated with reading DNA sequences and comparing sequences to finding common patterns. The author then considers that statistics of pattern counts in sequences, RNA secondary structure, and the inference of evolutionary history of related sequences.

    Introduction to Computational Biology exposes the reader to the fascinating structure of biological data and explains how to treat related combinatorial and statistical problems. Written to describe mathematical formulation and development, this book helps set the stage for even more, truly interdisciplinary work in biology.

    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
    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
    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
    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
    Minimum Free-energy Structures
    Consensus folding
    Trees and Sequences
    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
    Problem Solutions and Hints
    Mathematical Notation
    Algorithm Index
    Author Index
    Subject Index


    Waterman, Michael S.

    "I very much enjoyed the book, and was delighted to recommend it…the use of molecular biology to introduce and illustrate application of sophisticated mathematical theory was excellent…as an illustration of the challenges and rewards of collaborative work, it is ideal."
    -Statistics: Monash University