A parallel algorithm for the fixed-length approximate string matching problem for high throughput sequencing technologies

Costas S. Iliopoulos, Laurent Mouchard, Solon P. Pissis

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

Abstract

The approximate string matching problem is to find all locations at which a query of length m matches a substring of a text of length n with k-or-fewer differences. Nowadays, with the advent of novel high throughput sequencing technologies, the approximate string matching algorithms are used to identify similarities, molecular functions and abnormalities in DNA sequences. We consider a generalization of this problem, the fixed-length approximate string matching problem: given a text t, a pattern ρ and an integer ℓ, compute the optimal alignment of all substrings of ρ of length ℓ and a substring of t. We present a practical parallel algorithm of comparable simplicity that requires only time, where w is the word size of the machine (e.g. 32 or 64 in practice) and p the number of processors, by virtue of computing a bit representation of the relocatable dynamic programming matrix for the problem. Thus the algorithm's performance is independent of k and the alphabet size |Σ|.

Original languageEnglish
Title of host publicationParallel Computing
Subtitle of host publicationFrom Multicores and GPU's to Petascale
PublisherIOS Press BV
Pages150-157
Number of pages8
ISBN (Print)9781607505297
DOIs
Publication statusPublished - 2010
Externally publishedYes

Publication series

NameAdvances in Parallel Computing
Volume19
ISSN (Print)0927-5452

Keywords

  • approximate string matching
  • high throughput sequencing technologies
  • parallel algorithms
  • string algorithms

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  • Cite this

    Iliopoulos, C. S., Mouchard, L., & Pissis, S. P. (2010). A parallel algorithm for the fixed-length approximate string matching problem for high throughput sequencing technologies. In Parallel Computing: From Multicores and GPU's to Petascale (pp. 150-157). (Advances in Parallel Computing; Vol. 19). IOS Press BV. https://doi.org/10.3233/978-1-60750-530-3-150