Indexing a dictionary for subset matching queries

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

We consider a subset matching variant of the Dictionary Query problem. Consider a dictionary D of n strings, where each string location contains a set of characters drawn from some alphabet E. Our goal is to preprocess D so when given a query pattern p, where each location in p contains a single character from Σ, we answer if p matches to D. p is said to match to D if there is some s ∈ D where |p| = |s| and p[i] ∈ s[i] for every 1 ≤ i ≤ |p|. To achieve a query time of O(|p|), we construct a compressed trie of all possible patterns that appear in D. Assuming that for every a ∈ D there are at most k locations where |s[i]| > 1, we present two constructions of the trie that yield a preprocessing time of O(nm + |Σ|k n lg(min{n, m})), where n is the number of strings in D and m is the maximum length of a string in D. The first construction is based on divide and conquer and the second construction uses ideas introduced in [2] for text fingerprinting. Furthermore, we show how to obtain O(nm + |Σ|k n + |Σ|k/2 n lg(min{n, m})) preprocessing time and O(|p|lg lg|Σ| + min{|p|lg(|Σ|kn)}lg lg(|Σ|kn)) query time by cutting the dictionary strings and constructing two compressed tries. Our problem is motivated by haplotype inference from a library of genotypes [14,17]. There, D is a known library of genotypes (|Σ| = 2), and p is a haplotype. Indexing all possible haplotypes that can be inferred from D as well as gathering statistical information about them can be used to accelerate various haplotype inference algorithms. In particular, algorithms based on the "pure parsimony criteria" [13,16], greedy heuristics such as "Clarks rule" [6,18], EM based algorithms [1,11,12,20,26,30], and algorithms for inferring haplotypes from a set of Trios [4,27].

Original languageEnglish
Title of host publicationString Processing and Information Retrieval - 14th International Symposium, SPIRE 2007, Proceedings
PublisherSpringer Verlag
Pages195-204
Number of pages10
ISBN (Print)9783540755296
DOIs
StatePublished - 2007
Event14th International Symposium on String Processing and Information Retrieval, SPIRE 2007 - Santiago, Chile
Duration: 29 Oct 200731 Oct 2007

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume4726 LNCS
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference14th International Symposium on String Processing and Information Retrieval, SPIRE 2007
Country/TerritoryChile
CitySantiago
Period29/10/0731/10/07

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Computer Science (all)

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