Unique marker finder algorithm generates molecular diagnostic markers

Abstract

By taking advantage of the power of comparative genomics, we devised an algorithm, Unique Marker Finder (U-MarFin), to generate a collection of unique DNA sequences from a target organism. The whole target genome is partitioned into a scoring pool of less 4000 base-pair fragments, which are then subjected to elimination of homologous sequences in other bacterial genomes by BLAST alignment, and looked for all open reading frames as they may be applied as unique markers. Through regular, nested, multiplex and real time PCR and microarray technology, we empirically demonstrated that the sequences discovered were highly specific to the species that they are derived from, and they can serve as molecular biomarkers for diagnostic purpose.