ProbeDesigner: for the design of probesets for branched DNA (bDNA) signal amplification assays.
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.
Bushnell
S
S
Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.
Budde
J
J
Catino
T
T
Cole
J
J
Derti
A
A
Kelso
R
R
Collins
M L
ML
Molino
G
G
Sheridan
P
P
Monahan
J
J
Urdea
M
M
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
D015342:DNA Probes; D004247:DNA