Genomes, Browsers and Databases: Data-Mining Tools for Integrated Genomic Databases by Peter Schattner

by Peter Schattner

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.

Paperback

First published June 1, 2008

About the author

Peter Schattner is a scientist, educator and writer with over 30 years of research experience that spanning diverse fields from molecular biology and genetics to biomedical instrumentation and theoretical physics. His work in molecular biology has ranged from designing computer programs that detect functional non-protein elements in DNA to developing algorithms that identify DNA regulatory regions. He was also responsible for the development of the instructional material for BioPerl, a widely used computer framework for DNA and protein analysis.

He received his Ph.D. from M.I.T under Nobel Laureate Steven Weinberg and has held research and teaching positions in computational biology, biomedical engineering and physics at the University of California, California State University, Stanford Research Institute and Diasonics, Inc., where he contributed to the early development of medical ultrasound and MRI scanners. He is the author of numerous scientific articles and reviews as well as the textbook Genomes, Browsers and Databases. He was a Woodrow Wilson Fellow and a winner of the American Institute of Ultrasound in Medicine’s Award for Technical Innovation. When not doing science, he enjoys hiking, music and wildlife photography. His first book for nonscientists Sex, Love and DNA: What Molecular Biology Teaches Us About Being Human will be published in September 2014.