by Jonathan Pevsner

Bioinformatics and Functional Genomics provides an important integrative approach to understanding both the theory and practice of the emerging field of bioinformatics. Broadly encompassing the field of bioinformatics, from sequence analysis, gene expression, microarrays, and proteomics to molecular phylogenics and whole genome studies, this groundbreaking text shows how bioinformatics applies to biological questions at different levels, such as gene/protein, disease, and protein structures.

Combining theoretical context with practical application, the author emphasizes practical skills, such as how to analyze genes and proteins, how to make trees using phylogenic software, how to extract data, and how to identify genes and proteins implicated in disease. In addition, the text provides:

• A systematic three-part format, beginning with the analysis of biological sequence data, continuing with functional genomics (from microarrays to proteomics), and ending with coverage of genomesthroughout the tree of life. The subject of the human genome concludes with the latest advances in bioinformatics approaches to human disease
• Chapter-by-chapter problem sets, Web exercises, and Web links, as well as references to freely available software and annotated lists of recommended reading
• Consistent use of an example of a gene and its protein product, retinal-binding protein (RBP)
• Highlighted references to related studies, such as those involving breast cancer and HIV-1
• Clear discussion of the positive and negative ramifications of the approaches covered

Although the text emphasizes the use of computational tools and databases, the author assumes no computational background, making this text an ideal reference for students at every level of study.

Contents

1. Analyzing DNA, RNA, and Protein Sequences in Databases
   1. Introduction
   2. Access to Sequence and Literature Databases
   3. Pairwise Sequence Alignment
   4. Basic Local Alignmnet Search Tool (BLAST)
   5. Advanced BLAST Searching

2. Genome-Wide Analysis of RNA and Protein
   6. Genome-wide Analysis of Gene Expression
   7. Gene Expression: Microarrays
   8. Protein Analysis and Proteomics
   9. Protein Structure
   10. Multiple Sequence Alignment
   11. Molecular Phylogeny

3. Genome Analysis
   12. Completed Genomes and the Tree of Life
   13. Completed Genomes: Viruses
   14. Completed Genomes: Bacteria and Archaea
   15. Eukaryotic Genomes: Fungi
   16. Eukaryotic Genomes: From Parasites to Primates
   17. The Human Genome
   18. Human Disease

Appendix: GCG for Protein and DNA Analysis
Glossary
Solutions to Self-Test Quizzes

Subject Index
Author Index

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