Fast filter-and-refine algorithms for subsequence selection

Large sequence databases, such as protein, DNA and gene sequences in biology, are becoming increasingly common. An important operation on a sequence database is approximate subsequence matching, where all subsequences that are within some distance from a given query string are retrieved. This paper proposes a filter-and-refine algorithm that enables efficient approximate subsequence matching in large DNA sequence databases. It employs a bitmap indexing structure to condense and encode each data sequence into a shorter index sequence. During query processing, the bitmap index is used to filter out most of the irrelevant subsequences, and false positives are removed in the final refinement step. Analytical and experimental studies show that the proposed strategy is capable of reducing response time substantially while incurring only a small space overhead.