On Applying String Matching in Searching Unique Oligonucleotides

In this paper we consider using string matching in finding unique, gene specific oligonucleotides, which can be used for example in genomic research involving polymerase chain reaction, gene cloning, microarray technology or antisense DNA studies. Because of the typically huge size of genomes, the practical speed of the method used is important. We tested both exact and approximate string matching methods and further developed some of them to achieve better run times. Then we used the methods seen to be the fastest to complete exhaustive unique oligonucleotide search for many of the currently sequenced genomes.