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" 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.


CONCLUSIONS
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/.
Chen
Shu-Hwa
SH
Stem Cell/Regenerative Medicine Program, Genomics Research Center, Academia Sinica, No, 128 Academia Rd, Sec. 2, Taipei 115, Taiwan. seven@gate.sinica.edu.tw
Lo
Chen-Zen
CZ
Tsai
Ming-Chi
MC
Hsiung
Chao A
CA
Lin
Chung-Yen
CY
D001483:Base Sequence; D015342:DNA Probes / Q000235:genetics*; D004867:Equipment Design; D019544:Equipment Failure Analysis; D018390:Gene Targeting / Q000379:methods*; D017403:In Situ Hybridization / Q000379:methods; D020407:Internet; D008969:Molecular Sequence Data; D020411:Oligonucleotide Array Sequence Analysis / Q000295:instrumentation* / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
D015342:DNA Probes