Elsevier

Journal of Discrete Algorithms

Volume 18, January 2013, Pages 113-122
Journal of Discrete Algorithms

Indexing hypertext

https://doi.org/10.1016/j.jda.2012.10.001Get rights and content
Under an Elsevier user license
open archive

Abstract

Recent advances in nucleic acid sequencing technologies have motivated research into succinct text indexes to represent reference genomes that support efficient pattern matching queries. Similarly, sequencing technologies can also produce reads (patterns) derived from transcripts which need to be aligned to a reference transcriptome. A transcriptome can be modeled as a hypertext—a generalization of a linear text to a graph where nodes contain text and edges denote which nodes can be concatenated. Motivated by this application, we propose the first succinct index for hypertext. The index can model any hypertext and places no restriction on the graph topology. We also propose a new exact pattern matching algorithm, capable of aligning a pattern to any path in the hypertext, that is especially efficient when few nodes of the hypertext share common prefixes or when each node has constant degree.

Keywords

Succinct text indexing
Hypertext
Pattern matching

Cited by (0)

A preliminary version of this work appeared in the 18th International Symposium on String Processing and Information Retrieval (SPIRE 2011).