TY - JOUR
T1 - UPS 2.0
T2 - Unique probe selector for probe design and oligonucleotide microarrays at the pangenomic/ genomic level
AU - Chen, Shu Hwa
AU - Lo, Chen Zen
AU - Su, Sheng Yao
AU - Kuo, Bao Han
AU - Hsiung, Chao A.
AU - Lin, Chung Yen
N1 - Funding Information:
The authors would like to thank the National Science Council of the Republic of China, Taiwan, for financially supporting this research under Contract Nos. NSC 98-2221-E-001-018 and NSC 98-3112-B-400-010. Yu-Bin Wang, Jan-Hrong Lu, and Chu-Fang Lo from National Taiwan University are appreciated for their works on experimental validation and Ted Knoy for his editorial assistance. This article has been published as part of BMC Genomics Volume 11 Supplement 4, 2010: Ninth International Conference on Bioinformatics (InCoB2010): Computational Biology. The full contents of the supplement are available online at http://www.biomedcentral.com/1471-2164/11?issue=S4.
PY - 2010/12/2
Y1 - 2010/12/2
N2 - Background: Nucleic acid hybridization is an extensively adopted principle in biomedical research, in which the performance of any hybridization-based method depends on the specificity of probes to their targets. To determine the optimal probe(s) for detecting target(s) from a sample cocktail, we developed a novel algorithm, which has been implemented into a web platform for probe designing. This probe design workflow is now upgraded to satisfy experiments that require a probe designing tool to take the increasing volume of sequence datasets.Results: Algorithms and probe parameters applied in UPS 2.0 include GC content, the secondary structure, melting temperature (Tm), the stability of the probe-target duplex estimated by the thermodynamic model, sequence complexity, similarity of probes to non-target sequences, and other empirical parameters used in the laboratory. Several probe background options,Unique probe within a group,Unique probe in a specific Unigene set,Unique probe based onthe pangenomic level, and Unique Probe in the user-defined genome/transcriptome, are available to meet the scenarios that the experiments will be conducted. Parameters, such as salt concentration and the lower-bound Tm of probes, are available for users to optimize their probe design query. Output files are available for download on the result page. Probes designed by the UPS algorithm are suitable for generating microarrays, and the performance of UPS-designed probes has been validated by experiments.Conclusions: The UPS 2.0 evaluates probe-to-target hybridization under a user-defined condition to ensure high-performance hybridization with minimal chance of non-specific binding at the pangenomic and genomic levels. The UPS algorithm mimics the target/non-target mixture in an experiment and is very useful in developing diagnostic kits and microarrays. The UPS 2.0 website has had more than 1,300 visits and 360,000 sequences performed the probe designing task in the last 30 months. It is freely accessible at http://array.iis.sinica.edu.tw/ups/.Screen cast: http://array.iis.sinica.edu.tw/ups/demo/demo.htm.
AB - Background: Nucleic acid hybridization is an extensively adopted principle in biomedical research, in which the performance of any hybridization-based method depends on the specificity of probes to their targets. To determine the optimal probe(s) for detecting target(s) from a sample cocktail, we developed a novel algorithm, which has been implemented into a web platform for probe designing. This probe design workflow is now upgraded to satisfy experiments that require a probe designing tool to take the increasing volume of sequence datasets.Results: Algorithms and probe parameters applied in UPS 2.0 include GC content, the secondary structure, melting temperature (Tm), the stability of the probe-target duplex estimated by the thermodynamic model, sequence complexity, similarity of probes to non-target sequences, and other empirical parameters used in the laboratory. Several probe background options,Unique probe within a group,Unique probe in a specific Unigene set,Unique probe based onthe pangenomic level, and Unique Probe in the user-defined genome/transcriptome, are available to meet the scenarios that the experiments will be conducted. Parameters, such as salt concentration and the lower-bound Tm of probes, are available for users to optimize their probe design query. Output files are available for download on the result page. Probes designed by the UPS algorithm are suitable for generating microarrays, and the performance of UPS-designed probes has been validated by experiments.Conclusions: The UPS 2.0 evaluates probe-to-target hybridization under a user-defined condition to ensure high-performance hybridization with minimal chance of non-specific binding at the pangenomic and genomic levels. The UPS algorithm mimics the target/non-target mixture in an experiment and is very useful in developing diagnostic kits and microarrays. The UPS 2.0 website has had more than 1,300 visits and 360,000 sequences performed the probe designing task in the last 30 months. It is freely accessible at http://array.iis.sinica.edu.tw/ups/.Screen cast: http://array.iis.sinica.edu.tw/ups/demo/demo.htm.
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U2 - 10.1186/1471-2164-11-S4-S6
DO - 10.1186/1471-2164-11-S4-S6
M3 - Article
C2 - 21143815
AN - SCOPUS:78649796984
SN - 1471-2164
VL - 11
JO - BMC Genomics
JF - BMC Genomics
IS - SUPPL. 4
M1 - S6
ER -