DASH: Searching Compressed DNA: Creating and Searching Compact Databases for The Genomic Era - Softcover

Gardner-Stephen, Paul

Softcover

ISBN 10: 3639121295 ISBN 13: 9783639121292

Publisher: VDM Verlag Dr. Müller, 2009

Synopsis

The advent of low-cost mass-sequencing of genomes presents significant data management difficulties. These will grow worse as it becomes routine to sequence the genomes of individual people and organisms, because existing systems store and search each genome separately. This approach is not feasible for searching and comparing the genomes of millions or billions of individual organisms. This book seeks to solve this problem by describing the DASH sequence alignment and compression algorithms. DASH makes use of the overwhelming similarities amongst genomes of a given species in order to compress, not only the database size, but also the index size and search time. The resulting novel approach to database compression, index compression, bioinformatics and information-retrieval should be of especial interest to anyone who has an interest in the storage and efficient searching of large data sets, whether DNA or any other subject which offers some degree of redundancy, such as natural language text or web pages.

About this title

About the Author

Dr. Paul Gardner-Stephen, BSc, PhD: Studied computer science (BSc) and bioinformatics (PhD) at Flinders University, Adelaide, Australia. Post doctoral fellow in bioinformatics and systems and network administrator at Flinders University, Adelaide, Australia.

Edition details

• Publisher: VDM Verlag Dr. Müller
• Publication date: 2009
• Language: English
• ISBN 10: 3639121295
• ISBN 13: 9783639121292
• Binding: Paperback
• Number of pages: 280