The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays

Background: Nucleic acid hybridization, a fundamental technique in molecular biology, can be modified into very effective and sensitive methods for detecting particular targets mixed with millions of non-target sequences. Therefore, avoiding cross-hybridization is the most crucial issue for developing diagnostic methods based on hybridization. Results: To develop a probe with a high discriminating power, this study constructed a web service, the Unique Probe Selector (UPS), for customized probe design. The UPS service integrates a probe design mechanism and a scoring system for evaluating the performance of probe annealing and the uniqueness of a probe in a user-defined genetic background. Starting from an intuitive web interface, the UPS accepts a query with single or multiple sequences in fasta format. The best probe(s) for each sequence can be downloaded from result pages in a fasta or .csv format with a summary of probe characteristics. The option "Unique probe within group&q...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Shu-Hwa Chen, Chen-Zen Lo, Ming-Chi Tsai, Chao A. Hsiung, Chung-Yen Lin
• Keywords: BMCBI 2008, Probe Design, Unique Probe, Unique Probe Selector