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Introduction to Computational Biology An Evolutionary Approach

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ISBN-10: 3764367008

ISBN-13: 9783764367008

Edition: 2006

Authors: Thomas Wiehe, Bernhard Haubold

List price: $69.95
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Description:

Analysis of molecular sequence data is the main subject of this introduction to computational biology. There are two closely connected aspects to biological sequences: (i) their relative position in the space of all other sequences, and (ii) their movement through this sequence space in evolutionary time. Accordingly, the first part of the book deals with classical methods of sequence analysis: pairwise alignment, exact string matching, multiple alignment, and hidden Markov models. In the second part evolutionary time takes center stage and phylogenetic reconstruction, the analysis of sequence variation, and the dynamics of genes in populations are explained in detail. In addition, the book…    
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Book details

List price: $69.95
Copyright year: 2006
Publisher: Birkh�user Boston
Publication date: 8/16/2007
Binding: Mixed Media
Pages: 328
Size: 7.00" wide x 9.50" long x 1.00" tall
Weight: 2.024
Language: English

Introduction
Reading and Writing
Design and Scope of This Book
Sequences in Space
Sequences in Time
Sequences in Space
Optimal Pairwise Alignment
What Is an Alignment?
Biological Interpretation of the Alignment Problem
Scoring Alignments
Amino Acid Substitution Matrices
PAM Matrices
BLOSUM Matrices
Comparison between PAM and BLOSUM
Application of Substitution Matrices
The Number of Possible Alignments
Global Alignment
Shotgun Sequencing and Overlap Alignment
Local Alignment
Accommodating Affine Gap Costs
Maximizing vs. Minimizing Scores
Example Application of Global, Local, and Overlap Alignment
Summary
Further Reading
Exercises and Software Demonstrations
Biological Sequences and the Exact String Matching Problem
Exact vs. Inexact String Matching
Naive Pattern Matching
String Searching in Linear Time
Trees
Set Matching Using Keyword Trees
Suffix Trees
Suffix Tree Construction
Suffix Arrays
Repetitive Sequences in Genomics-the C-value Paradox
Detection of Repeated and Unique Substrings Using Suffix Trees
Maximal Repeats
Generalized Suffix Tree
Longest Common Substring Problem
k-Mismatches
Summary
Further Reading
Exercises and Software Demonstrations
Fast Alignment: Genome Comparison and Database Searching
Global Alignment
Local Alignment
Global/Local Alignment: k-Error Matching
Examples of Database Search Programs
Database Composition
Heuristic vs. Optimal Alignment Methods
Application: Determining Gene Families
Statistics of Local Alignments
Maximum Local Alignment Scores
Choosing a Substitution Matrix
Bit Scores
Summary
Further Reading
Exercises and Software Demonstrations
Multiple Sequence Alignment
Scoring Multiple Alignments
Multiple Alignment by Dynamic Programming
Heuristic Multiple Alignment
Summary
Further Reading
Exercises and Study Questions
Sequence Profiles and Hidden Markov Models
Profile Analysis
Hidden Markov Models
Profile Hidden Markov Models
Summary
Further Reading
Exercises and Software Demonstration
Gene Prediction
What is a Gene?
Computational Gene Finding
Measuring the Accuracy of Gene Predictions
Ab initio Methods: Searching for Signals and Content
Codon Usage
Finding Splice Sites with a Sequence Profile
Exon Chaining
Comparative Methods
General Remarks
Comparative Gene Prediction at the Adh Locus
Problems and Perspectives
Summary
Further Reading
Exercises
Sequences in Time
Phylogeny
Is There a Tree?-Statistical Geometry
Likelihood-Mapping
The Number of Possible Phylogenies
Distance Methods
Average Linkage Clustering
Neighbor-Joining
Maximum Parsimony
Maximum Likelihood
Searching Through Tree Space
Nearest Neighbor Interchange
Subtree Pruning and Regrafting
Branch and Bound
Bootstrapping Phylogenies
Summary
Further Reading
Exercises and Study Questions
Sequence Variation and Molecular Evolution
The Record of Past Events
Mutations and Substitutions
The Molecular Clock
Explicit Models of Molecular Evolution
Estimating Evolutionary Rates
Coding Sequences: Synonymous and Non-Synonymous Substitutions
Substitutions in Globin Sequences
Applications of K[subscript a]/K[subscript s]
A Language Gene?
Selection in the Human Genome
Summary
Further Reading
Exercises
Genes in Populations: Forward in Time
Polymorphism and Genetic Diversity
The Neutral Theory
Modeling Evolution Forward in Time
The Neutral Wright-Fisher Model
Fixation and Loss of Alleles
The Hardy-Weinberg Law
Fixation Probability and Time to Fixation
Loss of Genetic Diversity
Adding Mutation to the Model
Finite Alleles Model
Infinite Alleles Model
Infinite Sites Model
Mutation Drift Balance
The Rate of Fixation
Number of Alleles
Genetic Diversity
Sampling Alleles from Populations
Ewens' Sampling Formula
Application
Selection
Summary
Further Reading
Exercises and Software Demonstration
Genes in Populations: Backward in Time
Individuals' Genealogies vs. Gene Genealogies
Forward vs. Backward in Time
The Coalescent
Coalescent vs. Phylogenetic Trees
The Infinite Sites Model and the Number of SNPs
Mathematical Properties of the Neutral Coalescent
Tree Depth, Tree Size and the Number of Segregating Sites
Heterozygosity
The Distribution of Segregating Sites
Simulation Example
Recombination
Selection
Combining Recombination and Selection
Summary
Further Reading
Software Demonstrations and Exercises
Testing Evolutionary Hypotheses
Hudson-Kreitman-Aguade (HKA) Test
Tajima's Test
Fu and Li's Test
McDonald-Kreitman Test
Minimum Number of Recombination Events
Detecting Linkage Disequilibrium
Implementations
Summary
Exercises and Software Demonstration
Bioinformer
Alignment
Protein Substitution Matrices
Number of Alignments
Pairwise Alignment
Match
String Matching
Suffix Tree
Repeat Searching
Hash Table
Dotplot
Probability
Hidden Markov Model
Evolution
Phylogeny
Drift
Wright-Fisher
Coalescent
Probability
Molecular Biology Figures and Tables
Resources
Answers to Exercises
References
Glossary
Author Index
Subject Index