title: 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.
authors: Department of Biology and Chemistry, City University of Hong Kong, Kowloon Tong, Hong Kong. kaychiu@cityu.edu.hk
authors: Sung-Kay
authors: SK
authors: Chiu
authors: Ming-Hua
authors: MH
authors: Hsieh
authors: Chi-Meng
authors: CM
authors: Tzeng
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology; D017931:DNA Primers / Q000235:genetics; D004269:DNA, Bacterial / Q000235:genetics / Q000302:isolation & purification; D004755:Enterobacteriaceae / Q000235:genetics; D004927:Escherichia coli Infections / Q000175:diagnosis; D019453:Escherichia coli O157 / Q000235:genetics; D005819:Genetic Markers; D006801:Humans; D009169:Mycobacterium tuberculosis / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis / Q000706:statistics & numerical data; D057089:Pathology, Molecular / Q000706:statistics & numerical data*; D016133:Polymerase Chain Reaction; D016415:Sequence Alignment / Q000706:statistics & numerical data; D014376:Tuberculosis / Q000175:diagnosis
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial; D005819:Genetic Markers