Computing for Comparative Microbial Genomics - Ussery, David Wayne

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Résumé :
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.

Sommaire:
Introductions.- Sequences as Biological Information: Cells Obey the Laws of Chemistry and Physics.- Bioinformatics for Microbiologists: An Introduction.- Microbial Genome Sequences: A New Era in Microbiology.- An Overview of Genome Databases.- The Challenges of Programming: A Brief Introduction.- Comparative Genomics.- Methods to Compare Genomes The First Examples.- Genomic Properties: Length, Base Composition and DNA Structures.- Word Frequencies and Repeats.- Transcriptomics and Proteomics.- Transcriptomics: Translated and Untranslated RNA.- Expression of Genes and Proteins.- Of Proteins, Genomes, and Proteomes.- Microbial Communities.- Microbial Communities: Core and Pan-Genomics.- Metagenomics of Microbial Communities.- Evolution of Microbial Communities; or, On the Origins of Bacterial Species.

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)