Sequential-Access FM-Indexes

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 $P$ 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.