Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists / Edition 1

Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists / Edition 1

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by David Wayne Ussery, Trudy M. Wassenaar, Stefano Borini
     
 

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ISBN-10: 1848002548

ISBN-13: 9781848002548

Pub. Date: 12/11/2008

Publisher: Springer London

The major difficulty many microbiologists face is simply that of too much information. As a result of sequencing technologies becoming so economical, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes.

This accessible text/reference provides a coherent set of tools and a

Overview

The major difficulty many microbiologists face is simply that of too much information. As a result of sequencing technologies becoming so economical, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes.

This accessible text/reference provides a coherent set of tools and a methodological framework for comparing raw DNA sequences and fully annotated genome sequences, then using these to build up and test models about groups of interacting organisms within an environment or ecological niche. Easy-to-follow, this introductory textbook is built around teaching computational / bioinformatics methods for comparison of microbial genomes, and includes detailed examples of how to compare them at the level of DNA, RNA, and protein, in terms of structural and functional analysis.

Topics and Features:

• Contains five introductory chapters each representing a specific scientific field, to bring all readers up to the same basic level

• Familiarizes readers with genome sequences, RNA sequences (transcriptomics), proteomics and regulation of gene expression

• Describes basic methods to compare genomes and visualize the results for easy interpretation

• Discusses microbial communities, providing a framework for analysing and comparing individual genomes or raw DNA derived from complete ecosystems

• Introduces various atlases, building up to the Genome Atlas

• Offers numerous helpful examples throughout

• Focuses on the use and interpretation of publicly available Web tools

• Provides supplemental resources, such as Web links, at http://comparativemicrobial.com

Developed from a set of lectures for a course in Comparative Microbial Genomics taught since 2001, this wide-ranging foundational textbook is aimed at advanced undergraduate and graduate students in Bioinformatics and Microbiology. The authors are from diverse backgrounds complementing the interdisciplinary nature of the topic and consequently have developed a common scientific language. Readers will find this text an invaluable reference for computational and bioinformatics tools.

Product Details

ISBN-13:
9781848002548
Publisher:
Springer London
Publication date:
12/11/2008
Series:
Computational Biology Series, #8
Edition description:
2009
Pages:
270
Product dimensions:
6.30(w) x 9.30(h) x 0.80(d)

Table of Contents

Preface v

Acknowledgements ix

Part I Introductions

1 Sequences as Biological Information: Cells Obey the Laws of Chemistry and Physics 3

Why Study Microbes? 3

What is Biological Information and Where Does It Come From 5

How DNA Sequences Code for Information 7

From DNA to Protein: Transcription and Translation 9

DNA Sequences: More than Protein-Coding Genes 12

From DNA to DNA: Replication 14

Proteins: Structure and Function 14

2 Bioinformatics for Microbiologists: An Introduction 19

Identifying Similarities: Sequence Comparison by Means of Alignments 19

From Alignments to Phylogenic Relationships 28

Genome Annotation: the Challenge to Get It Right 31

Information Beyond the Single Genome 33

3 Microbial Genome Sequences: A New Era in Microbiology 37

The First Completely Sequenced Microbial Genome 37

The Importance of Visualization 38

Genome Atlases to Visualize Chromosomes 42

A Race Against the Clock: The Speed of Sequencing 44

The First Completely Sequenced Bacterial Genome 46

Comparative Bacterial Genomics 47

The Microbial Genome: Not All Bacteria Are Like E. coli 50

4 An Overview of Genome Databases 53

What is a Database? 54

Three Databases Storing Sequences and a Lot More 57

Data Files and Formats 61

RNA Databases 62

Protein Databases 64

5 The Challenges of Programming: a Brief Introduction 69

Part 1 A Brief Overview of Computer Science Concepts 69

A Look at the Most Common Bioinformatic Procedures 73

Achieving Better Automation 81

Part 2 Some Technical Details and Future Directions 83

Programming Languages 83

Markup Languages 86

Service Oriented Architecture88

Specific Tools for Bioinformatic Use 89

Part II Comparative Genomics

6 Methods to Compare Genomes: the First Examples 95

Genomic Comparisons: The Size of a Genome 95

Pairwise Alignment of Genomes 99

Comparing Gene Content and Annotation Quality 100

RNA Comparisons: A Look at rRNAs 102

Proteome Comparisons: What Makes a Family? 103

7 Genomic Properties: Length, Base Composition and DNA Structures 111

Length of Genomes: the 'C-Value Paradox' 112

Genome Average Base Composition: The Percentage of At 114

GC Skew-Bias Towards The Replication Leading Strand 118

Global Chromosomal Bias of AT Content 122

DNA Structures 125

The Structure Atlas 128

Bias In Purines-A-DNA Atlases 129

More on Structure Atlases 131

8 Word Frequencies and Repeats 137

Analyzing Word Frequencies in a Genome 137

DNA Repeats Within a Chromosome 139

Introduction to the DNA Repeat Atlas 143

Local DNA Repeats are Related to Chromosomal AT Content 146

DNA Structures Related to Repeats in Sequences 147

The Genome Atlas: Our Standard Method for Visualization 147

Part III Transcriptomics and Proteomics

9 Transcriptomics: Translated and Untranslated RNA 153

Counting rRNA and tRNA Genes 154

A Closer Look at Ribosomal RNA 155

Genes Encoding Transfer RNA 160

Genes Coding mRNA: Comparing Codon Usage Between Bacteria 161

Other Non-coding RNA: tmRNA 164

10 Expression of Genes and Proteins 167

Comparing Gene Expression and Protein Expression 168

Part 1 Regulation of Transcription 169

Part 2 Regulation of Translation 179

Part 3 Protein Modification and Cellular Localization 180

Antigen and Epitope Prediction 185

11 Of Proteins, Genomes, and Proteomes 189

Part 1 Analysis of Individual Protein-Coding Genes 190

Part 2 How to Annotate a Complete Genome 197

Part 3 Proteome Comparisons 203

Part IV Microbial Communities

12 Microbial Communities: Core and Pan-Genomics 213

Defining Pan-Genomes and Core Genomes 214

Current Data Available for Pan- and Core Genome Analysis 218

The Pan- and Core Genome of Streptococcus 219

The Current Bacillus Pan- and Core Genome 221

An Overview of Some Proteobacterial Pan- and Core Genomes 222

The Burkholderia Pan- and Core Genome 223

13 Metagenomics of Microbial Communities 229

Metagenomics Based on 16S rRNA Analysis 230

Metagenomics Based on Complete DNA Sequencing 232

Environmental Influences on Base Composition 234

Visualization of Environmental Metagenomic Data 235

Marine Metagenomics 240

Other Metagenomics Applications 241

14 Evolution of Microbial Communities; or, On the Origins of Bacterial Species 243

Where Does Diversity Come From? 244

Evolution Takes Time 245

Evidence of Evolution in a Single Genome 247

Genome Islands 249

Evolution on a Chip 252

Species and Speciation: Vibrio cholerae 253

Can We Predict Evolution? Escherichia coli Genome Reduction 253

Abbreviations 257

Index 263

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