Handbook of Comparative Genomics: Principles and Methodology is a practical text for students and researchers covering basic and applied problems in the emerging field of comparative functional genomics. It offers a comparative perspective on the state of the art and key principles of genome sequencing, expression, evolution, and phylogenetics in organelles, prokaryotes, model organisms, and humans. Moreover, the Handbook provides a unique and thorough treatment of biological databases, analysis of the transcriptome and proteome, and the bioinformatic approaches for comparative genome analysis.The text begins with an introduction to important features of completely sequenced genomes from mitochondria, C. elegans and Arabidopsis to Drosophila and humans. The next section covers cutting-edge analytic approaches involving ESTs, SAGE, DNA microarrays, protein biochips, and 2D gel electrophoresis. The following section deals comprehensively with computational approaches to comparative genome and proteome sequence analysis, including sequence assembly, pattern searching, gene and protein function prediction, and structure prediction. The text concludes with a section discussing genome evolution and molecular phylogenetics. This timely and cutting-edge text also: * Presents both the concepts and methodology of comparative genomics * Reviews the basic principles of genomics and gene expression analysis * Covers the bioinformatics approaches to comparative analysis * Discusses analytic methods in proteomics and transcriptomics * Includes a comprehensive list of Web resourcesThe authors draw upon their wealth of teaching and research experience to offer a coherent presentation appropriate for students, trainees, researchers, and scientists across the life sciences.