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Bioinformatics, Vol 15, 348-355, Copyright © 1999 by Oxford University Press

ARTICLES

ProbeDesigner: for the design of probesets for branched DNA (bDNA) signal amplification assays

S Bushnell, J Budde, T Catino, J Cole, A Derti, R Kelso, ML Collins, G Molino, P Sheridan, J Monahan and M Urdea
Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.

MOTIVATION: 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. AVAILABILITY: The program is available as a commercial package through the Pharmaceutical Drug Discovery program at Chiron Diagnostics.
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