ArticleBMC bioinformatics2008
The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays.
Article in BMC bioinformatics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- ProBac-seq, a bacterial single-cell RNA sequencing methodology using droplet microfluidics and large oligonucleotide probe sets.Nature protocols · 2024Review
- UPS 2.0: unique probe selector for probe design and oligonucleotide microarrays at the pangenomic/genomic level.BMC genomics · 2010Article
- PrimerBank: a resource of human and mouse PCR primer pairs for gene expression detection and quantification.Nucleic acids research · 2010Article
- OligoArrayDb: pangenomic oligonucleotide microarray probe sets database.Nucleic acids research · 2009Article
- Bioinformatics research in the Asia Pacific: a 2007 update.BMC bioinformatics · 2008Article
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Authors and funding
5 authors.
Funding
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Abstract
backgroundNucleic 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.
resultsTo 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.
conclusionThe 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/.
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