Physical Sciences and Mathematics Commons^™

Dsim: A Distance-Based Indexing Method For Genomic Sequences, Xia Cao, Beng-Chin Ooi, Hwee Hwa Pang, Kian-Lee Tan, Anthony K. H. Tung

Research Collection School Of Computing and Information Systems

In this paper, we propose a Distance-based Sequence Indexing Method (DSIM) for indexing and searching genome databases. Borrowing the idea of video compression, we compress the genomic sequence database around a set of automatically selected reference words, formed from high-frequency data substrings and substrings in past queries. The compression captures the distance of each non-reference word in the database to some reference word. At runtime, a query is processed by comparing its substrings with the compressed data strings, through their distances to the reference words. We also propose an efficient scheme to incrementally update the reference words and the compressed …