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 language | English (US) |
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Pages (from-to) | 145-161 |
Number of pages | 17 |
Journal | International Journal of Bioinformatics Research and Applications |
Volume | 1 |
Issue number | 2 |
DOIs | |
State | Published - 2005 |
Externally published | Yes |
Keywords
- greedy algorithm
- setcover problem
- string barcoding
ASJC Scopus subject areas
- General Medicine