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On exact string matching of unique oligonucleotides.

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Author

Summary, in English

Unique, gene-specific oligonucleotides are used for many genetic investigations such as polymerase chain reaction, gene cloning, microarray technology and antisense DNA studies. It is a computationally demanding task to extract these oligonucleotides from DNA databases. We studied the problem from the point of view of the string matching problem. We implemented and tested several exact string matching algorithms and modified the implementations to be as effective as possible. Ten different implementations were tested on yeast genomic sequence data. The run times for the best algorithms were significantly improved compared to conventional approaches, while in principle, i.e. in respect of theoretical time complexity, these algorithms do not actually differ essentially from each other.

Publishing year

2005

Language

English

Pages

173-181

Publication/Series

Computers in Biology and Medicine

Volume

35

Issue

2

Document type

Journal article

Publisher

Elsevier

Topic

  • Medical Genetics

Keywords

  • Saccharomyces cerevisiae: genetics
  • Fungal: analysis
  • DNA
  • Oligonucleotides: genetics
  • Sequence Alignment: methods

Status

Published

ISBN/ISSN/Other

  • ISSN: 1879-0534