An index structure for spaced seed search

Authors:
Taku Onodera;Tetsuo Shibuya
Affiliations:
Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan;Human Genome Center, Institute of Medical Science, University of Tokyo, Tokyo, Japan
Venue:
ISAAC'11 Proceedings of the 22nd international conference on Algorithms and Computation
Year:
2011

Citing 10
Cited 1

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CPM'03 Proceedings of the 14th annual conference on Combinatorial pattern matching
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ICALP'03 Proceedings of the 30th international conference on Automata, languages and programming
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The gapped suffix array: a new index structure for fast approximate matching

SPIRE'10 Proceedings of the 17th international conference on String processing and information retrieval

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MLDM'13 Proceedings of the 9th international conference on Machine Learning and Data Mining in Pattern Recognition

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Abstract

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.