ProbeDesigner: for the design of probesets for branched DNA (bDNA) signal amplification assays
| Autor: | A. Derti, Jack Cole, M. Urdea, Steven Bushnell, Theodore J. Catino, P. Sheridan, Mark L. Collins, John E. Monahan, G. Molino, R. Kelso, J. Budde |
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| Rok vydání: | 1999 |
| Předmět: |
Statistics and Probability
Computer science Computational biology Biochemistry chemistry.chemical_compound Gene duplication BDNA test Animals Humans Molecular Biology Simulation Electronic Data Processing Hybridization probe Nucleic Acid Hybridization RNA DNA Nucleic acid amplification technique Computer Science Applications Computational Mathematics Computational Theory and Mathematics chemistry Complementarity (molecular biology) Primer (molecular biology) DNA Probes Nucleic Acid Amplification Techniques Signal amplification Software |
| Zdroj: | Bioinformatics. 15:348-355 |
| ISSN: | 1367-4811 1367-4803 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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