Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins

About this book

This fully revised Third Edition of a world-renowned classic provides a practical guide covering the full scope of key concepts in bioinformatics, from databases to predictive and comparative algorithms. With a new full-colour, enlarged page design, this edition offers the most readable, up-to-date, and thorough introduction to the field for biologists. All new features include special boxes, enhanced use of real examples, and expanded problem sets with answers provided on the book's dedicated Web site (www.wiley.com/bioinformatics).

Contents
Chapter 1. Sequence Databases (Rolf Apweiler).
Chapter 2. Mapping Databases (Tara Matise and Peter S. White).
Chapter 3. Information Retrieval from Biological Databases (Andreas D. Baxevanis).
Chapter 4. Genomic Databases (Tyra Wolfsberg).
Chapter 5. Predictive Methods Using DNA Sequences (Roderic Guigo and Enrique Blanco).
Chapter 6. Predictive Methods Using RNA Sequences (Michael Zucker and David Mathews).
Chapter 7. Sequence Polymorphisms (James C. Mullikin and Stephen T. Sherry).
Chapter 8. Predictive Methods Using Protein Sequences (Burkhard Rost and Yanay Ofran).
Chapter 9. Protein Structure Prediction and Analysis (David Wishart).
Chapter 10. Intermolecular Interactions and Biological Pathways (Gary D. Bader and Anton J. Enright).
Chapter 11. Assessing Pairwise Sequence Similarity: BLAST and FASTA (Andreas D. Baxevanis).
Chapter 12. Creation and Analysis of Protein Multiple Sequence Alignments (Geoffrey J. Barton).
Chapter 13. Sequence Assembly and Finishing Methods (Gerard Bouffard, Nancy F. Hansen, and Pamela Jacques Thomas).
Chapter 14. Phylogenetic Analysis (Fiona S. L. Brinkman).
Chapter 15. Computational Approaches in Comparative Genomics (Andreas D. Baxevanis).
Chapter 16. Microarray Analysis (John Quackenbush)
Chapter 17. Proteomics and Protein Identification (Michael Giddings, Mark R. Holmes, and Kevin Ramkissoon).
Chapter 18. Using Perl to Facilitate Biological Analysis (Lincoln D. Stein).

Contents

Foreword. Preface. Contributors. Bioinformatics and the Internet (A. Baxevanis). The NCBI Data Model (J. Ostell, et al.). The GenBank Sequence Database (I. Karsch--Mizrachi & B. Ouellette). Submitting DNA Sequences to the Databases (J. Kans & B. Ouellette). Structure Databases (C. Hogue). Genomic Mapping and Mapping Databases (P. White & T. Matise). Information Retrieval from Biological Databases (A. Baxevanis). Sequence Alignment and Database Searching (G. Schuler). Creation and Analysis of Protein Multiple Sequence Alignments (G. Barton). Predictive Methods Using DNA Sequences (A. Baxevanis). Predictive Methods Using Protein Sequences (S. Banerjee--Basu & A. Baxevanis). Expressed Sequence Tags (ESTs) (T. Wolfsberg & D. Landsman). Sequence Assembly and Finishing Methods (R. Staden, et al.). Phylogenetic Analysis (F. Brinkman & D. Leipe). Comparative Genome Analysis (M. Galperin & E. Koonin). Large--Scale Genome Analysis (P. Meltzer). Using Perl to Facilitate Biological Analysis (L. Stein). Glossary. Index.

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Biography

Andreas D. Baxevanis, Ph.D. is the Deputy Director for Intramural Research and the Director of the Computational Genomics Program at the National Human Genome Research Institute, National Institutes of Health. He is currently the editor-in-chief of Current Protocols in Bioinformatics, senior editor of Molecular Cancer Therapeutics, and associate editor of Proteins: Structure, Function, and Bioinformatics. His involvement in educational activities include teaching bioinformatics at The Johns Hopkins University, serving as adjunct faculty at Boston University, lecturing in numerous courses, and developing materials intended to facilitate the use of genomic sequence data. He is the recipient of the Bodossaki Foundation's 2000 Academic Prize in Medicine and Biology. Dr. B. F. Francis Ouellette is Director of the University of British Columbia Bioinformatics Centre and Director for the Canadian Genetic Disease Network (CGDN) Bioinformatics Facility, where he coordinates the Canadian Bioinformatics Workshop series. His research includes work on the Biomolecular Interaction Network Database (BIND), development of gene prediction tools, and use of comparative genomics approaches to help identify human genes. Dr. Ouellette has worked on yeast genome sequencing and analysis, and has previously served as GenBank coordinator at the National Center for Biotechnology Information (NCBI), NIH.