On exact string matching of unique oligonucleotides

Comput Biol Med. 2005 Feb;35(2):173-81. doi: 10.1016/j.compbiomed.2003.11.003.


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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • DNA, Fungal / analysis*
  • Oligonucleotides / genetics*
  • Saccharomyces cerevisiae / genetics
  • Sequence Alignment / methods*


  • DNA, Fungal
  • Oligonucleotides