Genetic Databases

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Overview

Computer access is the only way to retrieve up-to-date nucleic acid and protein sequence and structure information.
This book, edited by Martin Bishop, describes the available information and where to find it, and is essential reading for any researcher puzzled by the wealth of on-line data.
The reader will be guided through the maze of URLs, sites and searches to reach information on:
• DNA, RNA, protein sequence, and structure databases
• Sequence comparison and alignmen
• Phenotype, mutation and genetic linkage databases
• Simple repetitive DNA sequences
• Gene feature identification
• Prediction of structure and function of proteins from sequence information
The book includes a directory of URLs for easy reference and it will be invaluable to those starting a career in life sciences research and also for established researchers wishing to make full use of available resources.

Audience: Graduates and researchers in genetics, biochemistry, molecular biology, cell biology, immunology, microbiology - any discipline using molecular biology in their research. There is also the possibility of promotion to specific courses, most of which are fairly new. In the US there are 84 courses on 'Computers in Medicine' and 30 courses on 'Computer Applications in Health'. There are also 2 graduate courses in the UK on bioinformatics.

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Editorial Reviews

From the Publisher
"Read the book from cover to cover... is rewarding and provides one with a feel for the state of the art in relation to data mining from genetics databases... I would highly recommend the book to anyone currently doing research in the biological sciences and molecular or genetic science in particular" - Today's Life Sciences
Lynn Jablonski
...Martin Bishop has done a nice job assembling specialists in their fields who can explain the rationale, strenths, and weaknesses of many types of analysis used in bioinformatics... Overall, this would be a good book for use as an introductory bioinformatics text or for anyone who has an interest in learning various approaches to both eukaryotic and prokaryotic genome analysis...
ASM News
Michael Cummings
Genome projects and recombinant DNA technology are generating an avalanche of information. Using this information, we are able to identify, define, and characterize all the genes in a genome. In addition, we can predict the amino acid sequence of their gene products, and study the interaction, function, and location of these gene products. The new field of bioinformatics has developed in parallel with genome projects and has become one of the main tools used in the analysis of genome information. This book is a guide to the proliferating databases in which genetic information is stored. Because these resources are proliferating at a rapid rate, the editor has not attempted to provide an exhaustive list of all genetic databases. Rather, he has organized them by database type, providing an overview of the information contained in each, and how they are used. This book is for anyone, either experienced or novice, who wishes to access a new database. The book contains 15 chapters, and after an introduction, the editor begins with a description of nucleic acid and protein databases, followed by chapter contributions on phenotypic, mutation, linkage databases, codon usage, sequence comparison databases, and several other resources. Each chapter contributor provides an overview of the databases with instructions on how to use them, along with tables listing the URLs for many databases. All the URLs listed in the chapters are gathered into an appendix -- a single source for finding a specific site. Some chapters contain exercises, detailed examples, and instructions for accessing databases and submitting information. Anyone, from graduate student to experienced researcher andclinician, who has mouse-clicked his or her way into a genetic database only to be rapidly overwhelmed and frustrated by the lack of user-friendly instructions will find this to be a well-written guide. The editor provides an overview of what information is available, as well as general instructions on how to access the database and extract information. A few minutes of reading will reduce the time and frustration for novices as well as experienced users who wish to access a new database.
From The Critics
Reviewer:Michael Cummings, PhD (University of Illinois at Chicago)
Description:Genome projects and recombinant DNA technology are generating an avalanche of information. Using this information, we are able to identify, define, and characterize all the genes in a genome. In addition, we can predict the amino acid sequence of their gene products, and study the interaction, function, and location of these gene products. The new field of bioinformatics has developed in parallel with genome projects and has become one of the main tools used in the analysis of genome information.
Purpose:This book is a guide to the proliferating databases in which genetic information is stored. Because these resources are proliferating at a rapid rate, the editor has not attempted to provide an exhaustive list of all genetic databases. Rather, he has organized them by database type, providing an overview of the information contained in each, and how they are used.
Audience:This book is for anyone, either experienced or novice, who wishes to access a new database.
Features:The book contains 15 chapters, and after an introduction, the editor begins with a description of nucleic acid and protein databases, followed by chapter contributions on phenotypic, mutation, linkage databases, codon usage, sequence comparison databases, and several other resources. Each chapter contributor provides an overview of the databases with instructions on how to use them, along with tables listing the URLs for many databases. All the URLs listed in the chapters are gathered into an appendix — a single source for finding a specific site. Some chapterscontain exercises, detailed examples, and instructions for accessing databases and submitting information.
Assessment:Anyone, from graduate student to experienced researcher and clinician, who has mouse-clicked his or her way into a genetic database only to be rapidly overwhelmed and frustrated by the lack of user-friendly instructions will find this to be a well-written guide. The editor provides an overview of what information is available, as well as general instructions on how to access the database and extract information. A few minutes of reading will reduce the time and frustration for novices as well as experienced users who wish to access a new database.
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Product Details

  • ISBN-13: 9780121016258
  • Publisher: Elsevier Science
  • Publication date: 9/13/1999
  • Series: Biological Techniques Series
  • Edition description: SPIRAL
  • Pages: 320
  • Product dimensions: 0.81 (w) x 6.00 (h) x 9.00 (d)

Meet the Author

Martin Bishop works for the British Medicinal Resource Council as Bioinformatics Manager at the U.K. Human Genome Mapping Project Resource Centre.

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Table of Contents

M. Bishop, Introduction.
G. Williams, Nucleic Acid and Protein Sequence Databases.
R. Cotton, Phenotype, Mutation, and Genetic Linkage Databases and Their Links to Sequence Databases.
R. Guigo, DNA Composition, Codon Usage, and Exon Prediction.
W. Taylor, Properties of Amino Acids in Sequences.
M. Gribskov, Sequence Comparison.
J. Epplen, Simple Repetitive Sequences in DNA Databanks.
P. Bucher, Gene Feature Identification.
D. Higgins, Multiple Sequence Alignment.
K. Triman, RNAs.
C. Ponting and D.J. Blake, Predicting the Evolution, Structure, and Function of Proteins from Sequence Information.
D. Jones, Structure Databases and Structure Alignments.
M. Gribskov, Bourne, Smith, Integrated Data Resource for Protein Kinases.
R. Baldock, Gene Expression Databases.
P.D. Karp, Pathways and Development.

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