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, and can be easily parallelized to further extend the applicability range to thousands of bacterial size genomes. 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 language | English (US) |
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Pages (from-to) | 1020-1028 |
Number of pages | 9 |
Journal | Lecture Notes in Computer Science |
Volume | 3515 |
Issue number | II |
DOIs | |
State | Published - 2005 |
Externally published | Yes |
Event | 5th International Conference on Computational Science - ICCS 2005 - Atlanta, GA, United States Duration: May 22 2005 → May 25 2005 |
ASJC Scopus subject areas
- Theoretical Computer Science
- General Computer Science