Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists

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Springer Science & Business Media, 26 feb. 2009 - 270 páginas
Overview and Goals This book describes how to visualize and compare bacterial genomes. Sequencing technologies are becoming so inexpensive that soon going for a cup of coffee will be more expensive than sequencing a bacterial genome. Thus, there is a very real and pressing need for high-throughput computational methods to compare hundreds and thousands of bacterial genomes. It is a long road from molecular biology to systems biology, and in a sense this text can be thought of as a path bridging these ? elds. The goal of this book is to p- vide a coherent set of tools and a methodological framework for starting with raw DNA sequences and producing fully annotated genome sequences, and then using these to build up and test models about groups of interacting organisms within an environment or ecological niche. Organization and Features The text is divided into four main parts: Introduction, Comparative Genomics, Transcriptomics and Proteomics, and ? nally Microbial Communities. The ? rst ? ve chapters are introductions of various sorts. Each of these chapters represents an introduction to a speci? c scienti? c ? eld, to bring all readers up to the same basic level before proceeding on to the methods of comparing genomes. First, a brief overview of molecular biology and of the concept of sequences as biological inf- mation are given.
 

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Índice

Sequences as Biological Information Cells Obey the Laws of Chemistry and Physics
3
What is Biological Information and Where Does It Come From?
5
How DNA Sequences Code for Information
7
Transcription and Translation
9
More than ProteinCoding Genes
12
Replication
14
Bioinformatics for Microbiologists An Introduction
18
From Alignments to Phylogenic Relationships
28
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
Transcriptomics and Proteomics
151
Transcriptomics Translated and Untranslated RNA
152
Counting rRNA and tRNA Genes
154
A Closer Look at Ribosomal RNA
155

the Challenge to Get It Right
31
Information Beyond the Single Genome
33
Microbial Genome Sequences A New Era
37
The Importance of Visualization
38
Genome Atlases to Visualize Chromosomes
42
The Speed of Sequencing
44
The First Completely Sequenced Bacterial Genome
46
Comparative Bacterial Genomics
47
Not All Bacteria Are Like E coli
50
An Overview of Genome Databases
52
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
The Challenges of Programming A Brief Introduction
69
A Look at the Most Common Bioinformatic Procedures
73
Achieving Better Automation
81
Some Technical Details and Future Directions
83
Markup Languages
86
Service Oriented Architecture
88
Specific Tools for Bioinformatic Use
89
Comparative Genomics
92
Methods to Compare Genomes The First Examples
95
Pairwise Alignment of Genomes
99
Comparing Gene Content and Annotation Quality
100
A Look at rRNAs
102
What Makes a Family?
103
Genomic Properties Length Base Composition and DNA Structures
110
the CValue Paradox
112
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 ADNA Atlases
129
More on Structure Atlases
131
Word Frequencies and Repeats
137
Genes Encoding Transfer RNA
160
Comparing Codon Usage Between Bacteria
161
tmRNA
164
Expression of Genes and Proteins
167
Comparing Gene Expression and Protein Expression
168
Regulation of Transcription
169
Regulation of Translation
179
Protein Modification and Cellular Localization
180
Antigen and Epitope Prediction
185
Of Proteins Genomes and Proteomes
189
Analysis of Individual ProteinCoding Genes
190
How to Annotate a Complete Genome
197
Proteome Comparisons
203
Microbial Communities
211
Microbial Communities Core and PanGenomics
212
Defining PanGenomes 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
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 Metagenomic Applications
241
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
Vibrio cholerae
253
Abbreviations
257
Index
263
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