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Genomes, Browsers and Databases

Data-Mining Tools for Integrated Genomic Databases

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Paperback | 29 September 2008

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342 Pages

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25.4 x 17.78 x 1.8

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The recent explosive growth of biological data has lead to a rapid increase in the number of molecular biology databases. Held in many different locations and often using varying interfaces and non-standard data formats, integrating and comparing data from these multiple databases can be difficult and time-consuming. This book provides an overview of the key tools currently available for large-scale comparisons of gene sequences and annotations, focusing on the databases and tools from the University of California, Santa Cruz (UCSC), Ensembl, and the National Centre for Biotechnology Information (NCBI). Written specifically for biology and bioinformatics students and researchers, it aims to give an appreciation for the methods by which the browsers and their databases are constructed, enabling readers to determine which tool is the most appropriate for their requirements. Each chapter contains a summary and exercises to aid understanding and promote effective use of these important tools.

Industry Reviews

'The book would suit a bioinformatician wishing to gain an introduction into genome database querying and interaction.' Microbiology Today
'... provides a step-by-step account of how most commonly-used databases are compiled and updated, their applications and practical examples of how to use them. It is suitable for graduates and advanced undergraduates in bioinformatics or biology, or any researcher intent on exploiting the capabilities of databases as research tools more fully. ... the great strength of this book is its focus on basic concepts, with an emphasis on how to obtain information, enabling the reader to find new things out for themselves.' Journal of Biological Education

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Preface	p. ix
The Molecular Biology Data Explosion	p. 1
Introduction to Genome Browsing with the UCSC Genome Browser	p. 21
Browsing with Ensembl, MapViewer, and Other Genome Browsers	p. 38
Interactive Genome-Database Batch Querying	p. 61
Interactive Batch Post-Processing with Galaxy	p. 76
Introduction to Programmed Querying	p. 96
Using the Ensembl API	p. 102
Programmed Querying with Ensembl, Continued	p. 131
Introduction to the UCSC API	p. 148
More Advanced Applications Using the UCSC API	p. 178
Customized Genome Databases	p. 215
Genomes, Browsers, Databases - The Future	p. 238
Coordinate System Conventions	p. 253
Genome Data Formats	p. 259
UCSC Table Formats	p. 272
Genomic Sequence Alignments	p. 276
Program Code README File	p. 282
Selected General References for Genome Databases and Browers	p. 284
Online Documentation and Useful Web Sites for Genome Databases and Browsers	p. 288
Glossary of Biological and Computer Terms Used in the Text	p. 293
References	p. 307
Index	p. 313
Table of Contents provided by Ingram. All Rights Reserved.

Genomes, Browsers and Databases

Data-Mining Tools for Integrated Genomic Databases

At a Glance

Paperback

Industry Reviews

Shipping

How to return your order

Defective items

You Can Find This Book In

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