Computing for Comparative Microbial Genomics: Bioinformatics for MicrobiologistsSpringer 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. |
Índice
Cells Obey the Laws | 3 |
a Brief Introduction | 5 |
Structure and Function | 14 |
the Challenge to Get It Right | 28 |
An Overview of Genome Databases | 52 |
Length Base Composition | 110 |
Word Frequencies and Repeats | 137 |
Translated and Untranslated | 152 |
Expression of Genes and Proteins | 167 |
Of Proteins Genomes and Proteomes | 190 |
How to Annotate a Complete Genome Part 3 Proteome Comparisons | 197 |
Core and PanGenomics | 212 |
Metagenomics of Microbial Communities | 229 |
Evolution of Microbial Communities or On the Origins | 243 |
Abbreviations | 257 |
Otras ediciones - Ver todo
Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists David Wayne Ussery,Trudy M. Wassenaar,Stefano Borini Vista previa restringida - 2008 |
Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists David Wayne Ussery,Trudy M. Wassenaar,Stefano Borini No hay ninguna vista previa disponible - 2009 |
Computing for Comparative Microbial Genomics: Bioinformatics for Microbiologists David Wayne Ussery,Trudy M. Wassenaar,Stefano Borini No hay ninguna vista previa disponible - 2010 |
Términos y frases comunes
16S rRNA accession number Actinobacteria alignment amino acids analysis annotation archaea AT-rich Atlases bacterium Base Atlas base composition binding bioinformatics biological BLAST Atlas Burkholderia cell Chapter chromosome CLUSTALW codon usage color comparative genomics conserved contains core genome database dev avg DNA sequence encoded enzyme Escherichia coli eukaryotic evolution example FASTA figure Firmicutes frequently function GC skew GenBank genetic Genome Atlas Genome islands genome sequence global inverted repeats helix identify inverted repeats lane metadata metagenomic molecular molecules mRNA multiple NCBI nucleotide number of genes ORFs organisms palindromes pan-genome particular pathogen phyla plasmid plot PMID polymerase Position Preference predicted present produced protein sequences Proteobacteria proteome pseudomallei purine query reference genome regions represented ribosome rRNA rRNA genes rRNA operons secretion sequenced genomes shown in Fig shows sigma factors similar Stacking Energy strain strand Structure Atlas Swiss-Prot transcription translation tRNA visualization