Title: Unique marker finder algorithm generates molecular diagnostic markers

Authors: Sung-Kay Chiu, Ming-Hua Hsieh, Chi-Meng Tzeng

Addresses: Department of Biology and Chemistry, Academic Building, City University of Hong Kong, 83 Tat Chee Avenue, Kowloon Tong, Hong Kong. ' Department of Risk Management and Insurance, National Chengchi University, No. 64, Sec. 2, ZhiNan Rd., Wenshan District, Taipei City 11605, Taiwan. ' Department of Translation Medicine, Institute for Biomedical Research, Xiamen University, 361005, China

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.

Keywords: comparative genomics; subtraction; diagnostic markers; microarray; real-time PCR; DNA sequences; molecular biomarkers; polymerase chain reaction; bioinformatics.

DOI: 10.1504/IJBRA.2011.039168

International Journal of Bioinformatics Research and Applications, 2011 Vol.7 No.1, pp.24 - 42

Received: 01 Dec 2009
Accepted: 09 Jul 2010
Published online: 24 Jan 2015 *

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