title: ProbeDesigner: for the design of probesets for branched DNA (bDNA) signal amplification assays.
abstract: BACKGROUND
  The sensitivity and specificity of branched DNA (bDNA) assays are derived in part through the judicious design of the capture and label extender probes. To minimize non-specific hybridization (NSH) events, which elevate assay background, candidate probes must be computer screened for complementarity with generic sequences present in the assay.
  
  
  RESULTS
  We present a software application which allows for rapid and flexible design of bDNA probesets for novel targets. It includes an algorithm for estimating the magnitude of NSH contribution to background, a mechanism for removing probes with elevated contributions, a methodology for the simultaneous design of probesets for multiple targets, and a graphical user interface which guides the user through the design steps.
  
  
  BACKGROUND
  The program is available as a commercial package through the Pharmaceutical Drug Discovery program at Chiron Diagnostics.
authors.affiliation: Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.
authors.forename: S
authors.initials: S
authors.lastname: Bushnell
authors.forename: J
authors.initials: J
authors.lastname: Budde
authors.forename: T
authors.initials: T
authors.lastname: Catino
authors.forename: J
authors.initials: J
authors.lastname: Cole
authors.forename: A
authors.initials: A
authors.lastname: Derti
authors.forename: R
authors.initials: R
authors.lastname: Kelso
authors.forename: M L
authors.initials: ML
authors.lastname: Collins
authors.forename: G
authors.initials: G
authors.lastname: Molino
authors.forename: P
authors.initials: P
authors.lastname: Sheridan
authors.forename: J
authors.initials: J
authors.lastname: Monahan
authors.forename: M
authors.initials: M
authors.lastname: Urdea
mesh_terms: D000818:Animals; D004247:DNA / Q000032:analysis*; D015342:DNA Probes; D001330:Electronic Data Processing; D006801:Humans; D021141:Nucleic Acid Amplification Techniques; D009693:Nucleic Acid Hybridization / Q000379:methods*; D012984:Software
chemical_list: D015342:DNA Probes; D004247:DNA