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Dictionary Matching in Elastic-Degenerate Texts with Applications in Searching VCF Files On-line

Authors Solon P. Pissis, Ahmad Retha



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Solon P. Pissis
  • Department of Informatics, King’s College London, London, UK
Ahmad Retha
  • Department of Informatics, King’s College London, London, UK

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Solon P. Pissis and Ahmad Retha. Dictionary Matching in Elastic-Degenerate Texts with Applications in Searching VCF Files On-line. In 17th International Symposium on Experimental Algorithms (SEA 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 103, pp. 16:1-16:14, Schloss Dagstuhl - Leibniz-Zentrum für Informatik (2018)
https://doi.org/10.4230/LIPIcs.SEA.2018.16

Abstract

An elastic-degenerate string is a sequence of n sets of strings of total length N. It has been introduced to represent multiple sequence alignments of closely-related sequences in a compact form. For a standard pattern of length m, pattern matching in an elastic-degenerate text can be solved on-line in time O(nm^2+N) with pre-processing time and space O(m) (Grossi et al., CPM 2017). A fast bit-vector algorithm requiring time O(N * ceil[m/w]) with pre-processing time and space O(m * ceil[m/w]), where w is the size of the computer word, was also presented. In this paper we consider the same problem for a set of patterns of total length M. A straightforward generalization of the existing bit-vector algorithm would require time O(N * ceil[M/w]) with pre-processing time and space O(M * ceil[M/w]), which is prohibitive in practice. We present a new on-line O(N * ceil[M/w])-time algorithm with pre-processing time and space O(M). We present experimental results using both synthetic and real data demonstrating the performance of the algorithm. We further demonstrate a real application of our algorithm in a pipeline for discovery and verification of minimal absent words (MAWs) in the human genome showing that a significant number of previously discovered MAWs are in fact false-positives when a population's variants are considered.

Subject Classification

ACM Subject Classification
  • Theory of computation → Pattern matching
Keywords
  • on-line algorithms
  • algorithms on strings
  • dictionary matching
  • elastic-degenerate string
  • Variant Call Format

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