An Index Structure for Spaced Seed Search

  • Taku Onodera
  • Tetsuo Shibuya
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7074)


In this paper, we introduce an index structure of texts which supports fast search of patterns with “don’t care”s in predetermined positions. This data structure is a generalization of the suffix array and has many applications especially for computational biology. We propose three algorithms to construct the index. Two of them are based on a variant of radix sort but each utilizes different types of referential information to sort suffixes by multiple characters at a time. The other is for the case when “don’t care”s appear periodically in patterns and can be combined with the others.


Index Structure Binary String Fast Search Empty String Suffix Array 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2011

Authors and Affiliations

  • Taku Onodera
    • 1
  • Tetsuo Shibuya
    • 1
  1. 1.Human Genome Center, Institute of Medical ScienceUniversity of TokyoTokyoJapan

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