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

Shu-Hwa Chen^*¹^,2 , Chen-Zen Lo² , Ming-Chi Tsai² , Chao A Hsiung³ and Chung-Yen Lin^*²^,3^,4

¹Stem Cell/Regenerative Medicine Program, Genomics Research Center, Academia Sinica., No. 128 Academia Rd., Sec. 2, Taipei 115, Taiwan

²Institute of Information Science, Academia Sinica, No. 128 Academia Rd., Sec. 2, Taipei 115, Taiwan

³Division of Biostatistics and Bioinformatics, National Health Research Institutes. No. 35 Keyan Rd. Zhunan, Miaoli County 350, Taiwan

⁴Institute of Fishery Science, College of Life Science, National Taiwan University, No. 1, Roosevelt Rd. Sec 4, Taipei, Taiwan

author email corresponding author email* Contributed equally

BMC Bioinformatics 2008, 9(Suppl 1):S8doi:10.1186/1471-2105-9-S1-S8


Published:	13 February 2008

Abstract

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" selects the most unique probe for each target sequence with low probability to hybridize to the other sequences in the same submitted query. The option "Unique probe in the specific organism" devises probes for each submitted sequence to identify its target among selected genetic backgrounds based on Unigene.

Conclusion

The UPS evaluates probe-to-target hybridization under a user-defined condition in silico to ensure high-performance hybridization and minimizes the possibility of non-specific reactions. UPS has been applied to design human arrays for gene expression studies and to develop several small arrays of gene families that were inferred as molecular signatures of cancer typing/staging or pathogen signatures. Notably, UPS is freely accessible at http://array.iis.sinica.edu.tw/ups/ webcite.