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

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This fully revised version of a world-renowned bestseller provides readers with a practical guide covering the full scope of key concepts in bioinformatics, from databases to predictive and comparative algorithms. Using relevant biological examples, the book provides background on and strategies for using many of the most powerful and commonly used computational approaches for biological discovery. This Third Edition reinforces key concepts that have stood the test of time while making the reader aware of new and important developments in this fast-moving field. With a new full-color and enlarged page design, Bioinformatics, Third Edition offers the most readable, up-to-date, and thorough introduction to the field for biologists.

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

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 (
From the Publisher
"A reference that should be in the personal library of any biologist who uses the Internet for the analysis of DNA and protein sequence data"—Science

"This book is a rich source of information on an exciting new research field. The book's practical orientation and lack of mathematical detail should make it particularly appealing to professional geneticists." --The Quarterly Review of Biology, June 1999

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Product Details

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

Meet the Author

About the Editors

Dr. Baxevanis is Associate Director for Intramural Research, and Director for Computational Genomics at the National Human Genome Research Institute, National Institutes of Health. He received his BS in biological sciences from Cornell University in 1984 and his PhD in the Department of Biology at The Johns Hopkins University in 1991. His research focuses on protein structure-function relationships, positional cloning, and the development of new methods for analysis of gene expression data. His accom-plishments have been recognized by the Bodossaki Foundation in Greece, who awarded him their 1999 Academic Prize in Medicine and Biology.
Dr. Ouellette is Director of the Bioinformatics Core facility at the Center for Molecular Medicine and Therapeutics, University of British Columbia, and Director of the Bioinformatics Core facility for the Canadian Genetic Diseases Network. He held the position of GenBank coordinator for the National Center for Biotechnology Information at the National Institutes of Health. He received his PhD from the Department of Biology at McGill University in 1991, and is the founder and moderator of bionet.molbio.yeast, a Usenet discussion forum for the yeast genomics community.

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Table of Contents

1 Sequence databases 3
2 Mapping databases 25
3 Information retrieval from biological databases 55
4 Genomic databases 81
5 Predictive methods using DNA sequences 115
6 Predictive methods using RNA sequences 143
7 Sequence polymorphisms 171
8 Predictive methods using protein sequences 197
9 Protein structure prediction and analysis 223
10 Intermolecular interactions and biological pathways 253
11 Assessing pairwise sequence similarity : BLAST and FASTA 295
12 Creation and analysis of protein multiple sequence alignments 325
13 Sequence assembly and finishing methods 341
14 Phylogenetic analysis 365
15 Computational approaches in comparative genomics 393
16 Using DNA microarrays to assay gene expression 409
17 Proteomics and protein identification 445
18 Using Perl to facilitate biological analysis 475
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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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