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