Improved assay-dependent searching of nucleic acid sequence databases.
Improved assay-dependent searching of nucleic acid sequence databases.
复制标题
DOI：
10.1093/nar/gkn301
复制
发表时间：
2008-07
影响因子：
14.9
通讯作者：
Wolinsky M
中科院分区：
文献类型：
--
作者：
Gans JD;Wolinsky M
基于核酸的生物化学测定对现代生物学至关重要。关键应用，如细菌，病毒和真菌病原体的检测，需要详细的检测灵敏度和特异性的知识，以获得可靠的结果。需要改进的方法来预测测定性能，以利用呈指数增长的DNA序列数据量，并减少开发稳健的检测测定所需的实验工作。为此，我们提出了一种基于DNA热力学的序列相似性计算算法。在我们的方法中，搜索查询由代表杂交探针、一对挂锁探针或一对具有任选TaqMan™探针的PCR引物（即计算机模拟或“虚拟”PCR）的一至三个寡核苷酸序列组成。如果查询和靶标满足测定的热力学（在指定的杂交温度下结合和/或自由能的变化）和相关的生物学约束（测定序列以所需的方向与正确的靶标双链体链结合）两者，则报告匹配。我们的方法的灵敏度和特异性进行评估，通过比较预测的已知序列标记的位点在人类基因组中。自由能被证明是一个更敏感和具体的匹配标准比杂交温度。
Nucleic acid-based biochemical assays are crucial to modern biology. Key applications, such as detection of bacterial, viral and fungal pathogens, require detailed knowledge of assay sensitivity and specificity to obtain reliable results. Improved methods to predict assay performance are needed for exploiting the exponentially growing amount of DNA sequence data and for reducing the experimental effort required to develop robust detection assays. Toward this goal, we present an algorithm for the calculation of sequence similarity based on DNA thermodynamics. In our approach, search queries consist of one to three oligonucleotide sequences representing either a hybridization probe, a pair of Padlock probes or a pair of PCR primers with an optional TaqMan™ probe (i.e. in silico or ‘virtual’ PCR). Matches are reported if the query and target satisfy both the thermodynamics of the assay (binding at a specified hybridization temperature and/or change in free energy) and the relevant biological constraints (assay sequences binding to the correct target duplex strands in the required orientations). The sensitivity and specificity of our method is evaluated by comparing predicted to known sequence tagged sites in the human genome. Free energy is shown to be a more sensitive and specific match criterion than hybridization temperature.
登录
查看更多内容
影响因子：
3.5
作者：
Gyapay, G;Schmitt, K;Goodfellow, PN
通讯作者：
Goodfellow, PN
影响因子：
14.9
作者：
Rubin, E;Levy, AA
通讯作者：
Levy, AA
影响因子：
7
作者：
Stewart, EA;McKusick, KB;Cox, DR
通讯作者：
Cox, DR
影响因子：
5.8
作者：
Boutros, PC;Okey, AB
通讯作者：
Okey, AB
影响因子：
5.8
作者：
Murphy, K;Raj, T;White, PS
通讯作者：
White, PS