Computing for Comparative Microbial Genomics

Bioinformatics for Microbiologists

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

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The problem many microbiologists face is simply that of too much information. Built around teaching computational and bioinformatic methodology, this book details published methods for comparing genomes and provides examples of how to make custom comparisons.

Full Description

  • ISBN13: 978-1-8480-0254-8
  • 288 Pages
  • User Level: Students
  • Publication Date: December 16, 2008
  • Available eBook Formats: PDF
  • eBook Price: $89.95
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Full Description
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.
Table of Contents

Table of Contents

  1. Part I: Introductions.
  2. Sequences as Biological Information: Cells Obey the Laws of Chemistry and Physics.
  3. Bioinformatics for Microbiologists.
  4. Microbial Genome Sequences: A New Era in Microbiology.
  5. An Overview of Genome Databases.
  6. The Challenges of Programming: A Brief Introduction
  7. Part II: Comparative Genomics.
  8. Methods to Compare Genomes: The First Examples.
  9. Genome Length and DNA Base Composition.
  10. Word Frequencies, Repeats and Repeat
  11. related Structures.
  12. Part III: Transcriptomics and Proteomics.
  13. Transcriptomics: Translated and Untranslated RNA.
  14. Expression of Genes and Proteins.
  15. Of Proteins, Genomes and Proteomes.
  16. Part IV: Microbial Communities.
  17. Microbial Communities: Core and Pan
  18. genomics.
  19. Metagenomics of Microbial Communities.
  20. Evolution of Microbial Communities.
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