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 of 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.
1. The molecular biology data explosion; 2. Introduction to genome browsing with the UCSC Genome Browser; 3. Browsing with Ensembl, Map Viewer and other genome browsers; 4. Interactive genome-database batch querying; 5. Interactive batch post-processing with Galaxy; 6. Introduction to programmed querying; 7. Using the Ensembl API; 8. Programmed querying with Ensembl, continued; 9. Introduction to the UCSC API; 10. More advanced application using the UCSC API; 11. Customized genome databases; 12. Genomes, browsers, databases - the future.
Originally trained as a theoretical physicist, PETER SCHATTNER is currently a computational biologist at the University of California, Santa Cruz (UCSC). His principal research interests are in the genome-wide identification and characterization of non-protein-coding RNA genes and cis-regulatory mRNA motifs. Dr. Schattner has taught bioinformatics courses at the University of California and California State University and has worked in the research and development of medical ultrasound and magnetic resonance instrumentation at SRI (Stanford Research Institute) and Diasonics, Inc. He has been a Woodrow Wilson Fellow and was leader of the team that received the 1990 Matzuk Award for technical innovation from the American Institute of Ultrasound in Medicine.
'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