The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays.
The unique probe selector: a comprehensive web service for probe design and oligonucleotide arrays.
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独特的探针选择器：用于探针设计和寡核苷酸阵列的综合网络服务。
DOI：
10.1186/1471-2105-9-s1-s8
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发表时间：
2008
影响因子：
3
通讯作者：
Lin, Chung-Yen
中科院分区：
文献类型：
--
作者：
Chen, Shu-Hwa;Lo, Chen-Zen;Tsai, Ming-Chi;Hsiung, Chao A.;Lin, Chung-Yen
核酸杂交是分子生物学中的一项基本技术，可以改进为非常有效和灵敏的方法，用于检测与数百万非靶序列混合的特定靶。因此，避免交叉杂交是发展基于杂交的诊断方法的最关键问题。为了开发具有高鉴别力的探针，本研究构建了一个Web服务，独特的探针设计（UPS），定制的探针设计。UPS服务集成了探针设计机制和评分系统，用于评估探针退火的性能和探针在用户定义的遗传背景中的独特性。从直观的Web界面开始，UPS接受fasta格式的单个或多个序列的查询。每个序列的最佳探针可以从结果页面以fasta或.csv格式下载，并附有探针特征摘要。“组内唯一探针”选项为每个靶序列选择最独特的探针，其与同一提交查询中的其他序列杂交的概率较低。“特定生物体中的独特探针”选项为每个提交的序列设计探针，以根据Unigene在选定的遗传背景中识别其目标。UPS在用户定义的条件下通过计算机模拟评估探针与靶标杂交，以确保高性能杂交并最大限度地减少非特异性反应的可能性。UPS已被应用于设计用于基因表达研究的人类阵列，并开发了几个小的基因家族阵列，这些基因家族被推断为癌症分型/分期或病原体特征的分子特征。值得注意的是，UPS可在。
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. 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. 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 .