Computing for Comparative Microbial Genomics (eBook)

Bioinformatics for Microbiologists

Stefano Borini, David Wayne Ussery, Trudy M. Wassenaar (Autoren)

eBook Download: PDF

2008 | 1. Auflage
XIV, 274 Seiten
Springer London (Verlag)
978-1-84800-255-5 (ISBN)

Infos

The problem many microbiologists face is simply that of too much information. This book details many published methods for comparison of genomes, and provides examples of how custom comparisons can be made. The choice of methods obviously depends on the questions to be asked, and of course on the quantity of genomes to be compared. Two similar bacterial chromosomes can simply be aligned with each other, and regions of inversions and deletions can be readily visualised. However, this method won't work to compare hundreds of genomes, where 2-Dimensional clustering heat maps would be useful.



This text is built around teaching COMPUTATIONAL / BIOINFORMATIC 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 / functional analysis.



Aimed at advanced undergraduate and graduate students in Bioinformatics and Microbiology, this book will prove an invaluable reference to computational and bioinformatics tools.

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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.

Inhalt

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.

Produkt-Details

• Erscheint lt. Verlag: 22.10.2010
• Sprache: englisch
• Themenwelt: Informatik ► Theorie / Studium ► Künstliche Intelligenz / Robotik
• Themenwelt: Studium ► 2. Studienabschnitt (Klinik) ► Humangenetik
• Themenwelt: Naturwissenschaften ► Biologie ► Genetik / Molekularbiologie
• Themenwelt: Naturwissenschaften ► Biologie ► Mikrobiologie / Immunologie
• Schlagworte: Archaeal genomes • Bacterial genomes • Bioinformatics • chromosome • comparative genomics • Databases • DNA • Evolution • gene expression • Genome • heat map • metagenomes • Metagenomics • Microbiology • RNA
• ISBN-10: 1-84800-255-6 / 1848002556
• ISBN-13: 978-1-84800-255-5 / 9781848002555