Highly scalable algorithms for robust string barcoding

Bhaskar DasGupta, Kishori M. Konwar, Ion I. Mandoiu, Alex A. Shvartsman

Research output: Contribution to journalArticlepeer-review

Abstract

String barcoding is a recently introduced technique for genomic based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher selection based on whole genomic sequences of hundreds of microorganisms of up to bacterial size, on a well equipped workstation. Experimental results on both randomly generated and NCBI genomic data show that whole-genome based selection results in a number of distinguishers nearly matching the information theoretic lower bounds for the problem.

Original languageEnglish (US)
Pages (from-to)145-161
Number of pages17
JournalInternational Journal of Bioinformatics Research and Applications
Volume1
Issue number2
DOIs
StatePublished - 2005
Externally publishedYes

Keywords

  • greedy algorithm
  • setcover problem
  • string barcoding

ASJC Scopus subject areas

  • Medicine(all)

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