Introduction to Computational Biology: Maps, Sequences and Genomes, 1st Edition (Hardback) book cover

Introduction to Computational Biology

Maps, Sequences and Genomes, 1st Edition

By Michael S. Waterman

Chapman and Hall/CRC

448 pages

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Hardback: 9780412993916
pub: 1995-06-01
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Description

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.

Reviews

"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

Table of Contents

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

About the Series

Chapman & Hall/CRC Interdisciplinary Statistics

Learn more…

Subject Categories

BISAC Subject Codes/Headings:
MAT029000
MATHEMATICS / Probability & Statistics / General
SCI008000
SCIENCE / Life Sciences / Biology / General
SCI010000
SCIENCE / Biotechnology