
TL;DR
This paper introduces a method to improve the efficiency of querying FM-indexes stored in external memory by using auxiliary tables to enable sequential data access, reducing random access and potentially increasing speed.
Contribution
The paper presents a novel approach to FM-index querying that minimizes random disk access by leveraging auxiliary tables for sequential data retrieval.
Findings
Reduced random disk access during FM-index queries
Improved query speed due to sequential data access
Feasibility of efficient external memory FM-index querying
Abstract
Previous authors have shown how to build FM-indexes efficiently in external memory, but querying them efficiently remains an open problem. Searching na\"{i}vely for a pattern requires (\Theta (|P|)) random access. In this paper we show how, by storing a few small auxiliary tables, we can access data only in the order in which they appear on disk, which should be faster.
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Taxonomy
TopicsAlgorithms and Data Compression · Cellular Automata and Applications · DNA and Biological Computing
