Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins / Edition 3

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This fully revised Third Edition of a world-renowned classic provides readers with a practical guide covering the full scope of key concepts in bioinformatics, from databases to predictive and comparative algorithms. With a new full-color, 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 ( A glossary and appendix of sample file formats round out the book's reader-friendly, hands-on treatment.

Bioinformatics as a scientific discipline encompasses both an evolving conceptual basis as well as expanding methodology for the organization and analysis of sequence data. The second edition of this highly successful guide provides a review of the basic concepts along with discussions and comparisons of the available databases and computational analysis tools relevant to biological research.

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Editorial Reviews

From the Publisher
"…an outstanding achievement and will be a sound resource for bioengineers, cellular and molecular biotechnologists, and bioinformatists." (Annals of Biomedical Engineering, June 2006)

"…does an excellent job of tracking developments and providing an account that will be accessible to working biologists. This should be on the bookshelf of every molecular biologist." (The Quarterly Review of Biology, December 2005)

"...fully delivers on its promise of providing a useful and practical guide...I found it to be the most useful book on bioinformatics I have seen and recommend it very highly." (ASM News, September 2005)

“…not only an excellent guidebook … but also a supreme teaching and reference material.” (ChemBioChem, 2005; Vol. 6, 6)

"…not only an excellent guidebook for bioinformatics users but also…a supreme teaching and reference material." (ChemBioChem, July 4, 2005)

"…the most updated bioinformatics book that offers expert insights into cutting-edge tools of modern computational biology and stands out from many current texts on the subject." (American Journal of Human Biology, May/June 2005)

"…The book and the attached web links together give readers a rich resource of topics covered..." (Statistical Methods in Medical Research, Vol.14, No.1, 2005)

Nature Structural Biology
"... provides a broad overview of the basic tools for sequence analysis... For biologists approaching this subject for the first time, it will be a very useful handbook to keep on the shelf after the first reading, close to the computer."
"... should be in the personal library of any biologist who uses the Internet for the analysis of DNA and protein sequence data."
Trends in Biochemical Science
"... a wonderful primer designed to navigate the novice through the intricacies of in scripto analysis... The accomplished gene searcher will also find this book a useful addition to their library... an excellent reference to the principles of bioinformatics."
"... a useful resource to help biologists extract the maximum value from their data."
Biotech Software and Internet Report
"... a nice overview of ... bioinformatics that is suitable for the neophyte and those experienced in the field ... With the wide variety of topics covered, this book is one that should be included in the collection of anyone involved with the emerging field of bioinformatics."
Many of the contributors are from the Center for Biotechnology Information at the US National Institutes of Health, and others are scientists and instructors from around North America and Britain. Their work can be used as a classroom text, a tutorial, or a laboratory bench reference. No date is noted for the first edition, but the second reinforces concepts that have survived from the first, and incorporates new approaches and algorithms for analyzing genes and proteins. New chapters discuss expressed sequence tags, sequence assembly, comparative genomics, large-scale genome analysis, and BioPerl. Answers to the problems are available on a web site. Annotation c. Book News, Inc., Portland, OR (
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Product Details

  • ISBN-13: 9780471478782
  • Publisher: Wiley
  • Publication date: 10/22/2004
  • Edition description: REV
  • Edition number: 3
  • Pages: 560
  • Sales rank: 1,217,047
  • Product dimensions: 8.72 (w) x 11.08 (h) x 0.98 (d)

Meet the Author

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.

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Table of Contents

Foreword (Lee Hood).




1. Sequence Databases (Rolf Apweiler).

2. Mapping Databases (Peter S. White and Tara C. Matise).

3. Information Retrieval from Biological Databases (Andreas D. Baxevanis).

4. Genomic Databases (Tyra G. Wolfsberg).


5. Predictive Methods Using DNA Sequences (Enrique Blanco and Roderic Guigó).

6. Predictive Methods Using RNA Sequences (David Mathews and Michael Zuker).

7. Sequence Polymorphisms (James C. Mullikin and Stephen T. Sherry).


8. Predictive Methods Using Protein Sequences (Yanay Ofran and Burkhard Rost).

9. Protein Structure Prediction and Analysis (David Wishart).

10. Intermolecular Interactions and Biological Pathways (Gary D. Bader and Anton J. Enright).


11. Assessing Pairwise Sequence Similarity: BLAST and FASTA (Andreas D. Baxevanis).

12. Creation and Analysis of Protein Multiple Sequence Alignments (Geoffrey J. Barton).

13. Sequence Assembly and Finishing Methods (Nancy F. Hansen, Pamela Jacques Thomas and Gerard G. Bouffard).

14. Phylogenetic Analysis (Fiona S. L. Brinkman).

15. Computational Approaches in Comparative Genomics (Andreas D. Baxevanis).

16. Using DNA Microarrays to Assay Gene Expression (John Quackenbush).

17. Proteomics and Protein Identification (Mark R. Holmes, Kevin R. Ramkissoon and Morgan C. Giddings).


18. Using Perl to Facilitate Biological Analysis (Lincoln D. Stein).


Glossary. Index.

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"In this book, Andy Baxevanis and Francis Ouellette... have undertaken the difficult task of organizing the knowledge in this field in a logical progression and presenting it in a digestible form. And they have done an excellent job. This fine text will make a major impact on biological research and, in turn, on progress in biomedicine. We are all in their debt." (Eric Lander, from the Foreword)
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