title: A method for de novo nucleic acid diagnostic target discovery.
abstract: BACKGROUND
  A proper target or marker is essential in any diagnosis (e.g. an infection or cancer). An ideal diagnostic target should be both conserved in and unique to the pathogen. Currently, these targets can only be identified manually, which is time-consuming and usually error-prone. Because of the increasingly frequent occurrences of emerging epidemics and multidrug-resistant 'superbugs', a rapid diagnostic target identification process is needed.
  
  
  RESULTS
  A new method that can identify uniquely conserved regions (UCRs) as candidate diagnostic targets for a selected group of organisms solely from their genomic sequences has been developed and successfully tested. Using a sequence-indexing algorithm to identify UCRs and a k-mer integer-mapping model for computational efficiency, this method has successfully identified UCRs within the bacteria domain for 15 test groups, including pathogenic, probiotic, commensal and extremophilic bacterial species or strains. Based on the identified UCRs, new diagnostic primer sets were designed, and their specificity and efficiency were tested by polymerase chain reaction amplifications from both pure isolates and samples containing mixed cultures.
  
  
  METHODS
  The UCRs identified for the 15 bacterial species are now freely available at http://ucr.synblex.com. The source code of the programs used in this study is accessible at http://ucr.synblex.com/bacterialIdSourceCode.d.zip
  
  
  BACKGROUND
  yazhousun@synblex.com
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, PA 16802, Department of Research, Synblex LLC, 200 Innovation Blvd. State College, PA 16801 and New Jersey Center for Science, Technology & Mathematics, Kean University, Union, NJ 07083, USA Department of Biology, Pennsylvania State University, University Park, PA 16802, Department of Research, Synblex LLC, 200 Innovation Blvd. State College, PA 16801 and New Jersey Center for Science, Technology & Mathematics, Kean University, Union, NJ 07083, USA.
authors.forename: Yeting
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Biology, Pennsylvania State University, University Park, PA 16802, Department of Research, Synblex LLC, 200 Innovation Blvd. State College, PA 16801 and New Jersey Center for Science, Technology & Mathematics, Kean University, Union, NJ 07083, USA Department of Biology, Pennsylvania State University, University Park, PA 16802, Department of Research, Synblex LLC, 200 Innovation Blvd. State College, PA 16801 and New Jersey Center for Science, Technology & Mathematics, Kean University, Union, NJ 07083, USA.
authors.forename: Yazhou
authors.initials: Y
authors.lastname: Sun
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D017124:Conserved Sequence; D017931:DNA Primers; D004269:DNA, Bacterial / Q000737:chemistry; D016680:Genome, Bacterial; D023281:Genomics; D025202:Molecular Diagnostic Techniques; D016133:Polymerase Chain Reaction; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D017931:DNA Primers; D004269:DNA, Bacterial