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

Shu Hwa Chen, Chen Zen Lo, Ming Chi Tsai, Chao A. Hsiung, Chung Yen Lin

Research output: Contribution to journalArticle

7 Citations (Scopus)

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/.

Original languageEnglish
Article numberS8
JournalBMC Bioinformatics
Volume9
Issue numberSUPPL. 1
DOIs
Publication statusPublished - Feb 13 2008
Externally publishedYes

Fingerprint

Oligonucleotide Probes
Selector
Oligonucleotides
Oligonucleotide Array Sequence Analysis
Web services
Web Services
Probe
Nucleic Acid Hybridization
Neoplasm Staging
Computer Simulation
Molecular Biology
Gene Expression
Genes
Genetic Background
Design
Target
Signature
Query
Mechanism Design
Molecular biology

ASJC Scopus subject areas

  • Structural Biology
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Applied Mathematics

Cite this

The unique probe selector : A comprehensive web service for probe design and oligonucleotide arrays. / Chen, Shu Hwa; Lo, Chen Zen; Tsai, Ming Chi; Hsiung, Chao A.; Lin, Chung Yen.

In: BMC Bioinformatics, Vol. 9, No. SUPPL. 1, S8, 13.02.2008.

Research output: Contribution to journalArticle

Chen, Shu Hwa ; Lo, Chen Zen ; Tsai, Ming Chi ; Hsiung, Chao A. ; Lin, Chung Yen. / The unique probe selector : A comprehensive web service for probe design and oligonucleotide arrays. In: BMC Bioinformatics. 2008 ; Vol. 9, No. SUPPL. 1.
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