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

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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.

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Editorial Reviews

From the Publisher
From the reviews:

"It is a very well-written review of genomics and proteomics of microbes, and makes convincing arguments for the practicality of applying bioinformatics to the study of communities of these species. The references are well chosen. The writing style is superb. … There is an amazing amount of interesting material, in fewer than 275 pages. … The book is probably more suitable as an introduction to contemporary applications of bioinformatics and microbiology for computational scientists." (Anthony J. Duben, ACM Computing Reviews, June, 2009)

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Product Details

  • ISBN-13: 9781848002548
  • Publisher: Springer London
  • Publication date: 12/11/2008
  • Series: Computational Biology Series , #8
  • Edition description: 2009
  • Edition number: 1
  • Pages: 270
  • Product dimensions: 6.30 (w) x 9.30 (h) x 0.80 (d)

Table of Contents

Pt. I Introductions

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

2 Bioinformatics for Microbiologists: An Introduction 19

3 Microbial Genome Sequences: A New Era in Microbiology 37

4 An Overview of Genome Databases 53

5 The Challenges of Programming: a Brief Introduction 69

Pt. II Comparative Genomics

6 Methods to Compare Genomes: the First Examples 95

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

8 Word Frequencies and Repeats 137

Pt. III Transcriptomics and Proteomics

9 Transcriptomics: Translated and Untranslated RNA 153

10 Expression of Genes and Proteins 167

11 Of Proteins, Genomes, and Proteomes 189

Pt. IV Microbial Communities

12 Microbial Communities: Core and Pan-Genomics 213

13 Metagenomics of Microbial Communities 229

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

Abbreviations 257

Index 263

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