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.
Genomes, Browsers and Databases
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'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
'... 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
Book Description
Focusing on the databases and tools from the University of California, Santa Cruz (UCSC), Ensembl, and the National Centre for Biotechnology Information (NCBI), this book provides an overview of the key tools currently available for large-scale comparisons of gene sequences and annotations.
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1 of 1 people found the following review helpful:
5.0 out of 5 stars
Fundamental book for Genomics,
This review is from: Genomes, Browsers and Databases: Data-Mining Tools for Integrated Genomic Databases (Paperback)
The UCSC Genome Browser is a powerful tool that provides an open portal to the world's genomic information. But because its so powerful, it is often difficult to use. Here is an authoritative book that will get you on the air, not only with the reference data, but also with the means to compare it with your own data.
This is a terrific book.
2 of 3 people found the following review helpful:
4.0 out of 5 stars
powerful analytic tools,
By
This review is from: Genomes, Browsers and Databases: Data-Mining Tools for Integrated Genomic Databases (Hardcover)
The sheer mass of genetic data being assembled by various biotech firms and research labs has led to the rise of genomics. This book describes various computational tools currently available, to help the researcher analyse the data.
One such tool addresses the need to visualise. The brain is best at analysing large amounts of data when presented in visual form. Ensembl and MapViewer are 2 of the so-called genome browsers that have been written. They let you troll thru the data and see it displayed in several ways. While these might be called browsers, they are a far step from the generic web browsers. Be warned that the APIs have very nontrivial learning curves. Another part of the book looks at querying of databases. Another growing area, with sophisticated needs.
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Inside This Book
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Key Phrases - Statistically Improbable Phrases (SIPs):
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table browser, genome browser, other genome browsers, overlapping introns, intron length distributions, database adaptors, genome browsing, custom track, host introns, polymorphism site, transcript alignments, bed file, transcript object, skeleton database, annotation tracks, mirror database, intersection tool, database mirror, private mirror, local mirror, public mirror, chromosome name, void usage, query gene, other introns Key Phrases - Capitalized Phrases (CAPs): (learn more)
Gene Sorter, Ensembl Browser, Programmed Querying, Customized Genome Databases, Interactive Batch Post-Processing, Known Genes, Ensembl Perl, Havana Known Protein, The Molecular Biology Data Explosion, Interactive Genome-Database Batch Querying, Hello World, Mouse Genome Database, Genome Graphs, Basepair View, Pathway Tools, Exercises Note, Ensembl Intron, Ensembl Transcript, Ensembl Registry, Mouse Gut Community, Abundance Profiler, Detail View, Database Connection Test, Clone-based Intramural, Microsoft Windows Browse Sample Pages:
Front Cover | Table of Contents | First Pages | Index | Surprise Me!
table browser, genome browser, other genome browsers, overlapping introns, intron length distributions, database adaptors, genome browsing, custom track, host introns, polymorphism site, transcript alignments, bed file, transcript object, skeleton database, annotation tracks, mirror database, intersection tool, database mirror, private mirror, local mirror, public mirror, chromosome name, void usage, query gene, other introns Key Phrases - Capitalized Phrases (CAPs): (learn more)
Gene Sorter, Ensembl Browser, Programmed Querying, Customized Genome Databases, Interactive Batch Post-Processing, Known Genes, Ensembl Perl, Havana Known Protein, The Molecular Biology Data Explosion, Interactive Genome-Database Batch Querying, Hello World, Mouse Genome Database, Genome Graphs, Basepair View, Pathway Tools, Exercises Note, Ensembl Intron, Ensembl Transcript, Ensembl Registry, Mouse Gut Community, Abundance Profiler, Detail View, Database Connection Test, Clone-based Intramural, Microsoft Windows Browse Sample Pages:
Front Cover | Table of Contents | First Pages | Index | Surprise Me!
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