Efficient Querying on Genomic Databases by Using Metric Space Indexing Technology

The " Arbeitspapiere der GMD – GMD Technical Reports " primarily comprise preliminary publications , specific partial results and complementary material. In the interest of a subsequent final publication the " Arbeitspapiere/Technical Reports " should not be copied. Critical comments would be appreciated by the authors. No part of this publication may be reproduced or further processed in any form or by any means without the prior permission of GMD. All rights reserved. Abstract. A genomic database consists of a set of nucleotide sequences, for which an important kind of queries is the local sequence alignment. This paper studies the indexing techniques to support fast query evaluation for local alignment, by transforming the alignment problem to a variant metric space neighborhood search problem. We propose and analyze the corresponding algorithms and structures, and identify several directions for the future work.