Indexing hypertext

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.