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

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John Wiley & Sons, Mar 24, 2004 - Computers - 504 pages
4 Reviews
"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

Reviews from the First Edition

"...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."
Nature Structural Biology

"...should be in the personal library of any biologist who uses the Internet for the analysis of DNA and protein sequence data."
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."
Trends in Biochemical Sciences

This new edition of the highly successful Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins provides a sound foundation of basic concepts, with practical discussions and comparisons of both computational tools and databases relevant to biological research.

Equipping biologists with the modern tools necessary to solve practical problems in sequence data analysis, the Second Edition covers the broad spectrum of topics in bioinformatics, ranging from Internet concepts to predictive algorithms used on sequence, structure, and expression data. With chapters written by experts in the field, this up-to-date reference thoroughly covers vital concepts and is appropriate for both the novice and the experienced practitioner. Written in clear, simple language, the book is accessible to users without an advanced mathematical or computer science background. This new edition includes:

  • All new end-of-chapter Web resources, bibliographies, and problem sets
  • Accompanying Web site containing the answers to the problems, as well as links to relevant Web resources
  • New coverage of comparative genomics, large-scale genome analysis, sequence assembly, and expressed sequence tags
  • A glossary of commonly used terms in bioinformatics and genomics

Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, Second Edition is essential reading for researchers, instructors, and students of all levels in molecular biology and bioinformatics, as well as for investigators involved in genomics, positional cloning, clinical research, and computational biology.

 

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Contents

1 BIOINFORMATICS AND THE INTERNET
1
2 THE NCBI DATA MODEL
19
3 THE GENBANK SEQUENCE DATABASE
45
4 SUBMITTING DNA SEQUENCES TO THE DATABASES
65
5 STRUCTURE DATABASES
83
6 GENOMIC MAPPING AND MAPPING DATABASES
111
7 INFORMATION RETRIEVAL FROM BIOLOGICAL DATABASES
155
8 SEQUENCE ALIGNMENT AND DATABASE SEARCHING
187
11 PREDICTIVE METHODS USING PROTEIN SEQUENCES
253
12 EXPRESSED SEQUENCE TAGS ESTs
283
13 SEQUENCE ASSEMBLY AND FINISHING METHODS
303
14 PHYLOGENETIC ANALYSIS
323
15 COMPARATIVE GENOME ANALYSIS
359
16 LARGESCALE GENOME ANALYSIS
393
17 USING PERL TO FACILITATE BIOLOGICAL ANALYSIS
413
Glossary
451

9 CREATION AND ANALYSIS OF PROTEIN MULTIPLE SEQUENCE ALIGNMENTS
215
10 PREDICTIVE METHODS USING DNA SEQUENCES
233

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About the author (2004)

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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