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A Succinct Index for Hypertext

  • Chris Thachuk
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7024)

Abstract

Recent advances in nucleic acid sequencing technology has motivated research into succinct text indexes to represent reference genomes that support efficient pattern matching queries. Similar sequencing technology can also produce millions of reads (patterns) derived from transcripts which need to be aligned to a reference transcriptome. A transcriptome can be modeled as a hypertext. 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 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 the same text—in this important case, our algorithm is a significant improvement over all existing approaches.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Chris Thachuk
    • 1
  1. 1.Department of Computer ScienceUniversity of British ColumbiaVancouverCanada

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