Octamer-primed sequencing technology: development of primer identification software.
Octamer-primed sequencing technology: development of primer identification software.
复制标题
八聚体引物测序技术：引物识别软件的开发。
DOI：
10.1093/nar/28.7.e22
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发表时间：
2000
影响因子：
14.9
通讯作者：
Hardin,SH
中科院分区：
文献类型：
--
作者：
Mei,G;Hardin,SH
八聚体测序技术（OST）是一种引物指导的测序策略，其中从预合成的八聚体引物库中选择单个八聚体引物并用于对DNA片段进行测序。然而，从这样的文库中选择候选引物是耗时的，并且可能是测序过程中的瓶颈。为了加速测序过程并获得高质量的测序数据，开发了一种计算机程序，电子OST或eOST，以自动识别来自八聚体引物库的候选引物。eOST集成了碱基识别软件PHRED，可对靶序列进行质量评估，并识别位于高质量靶区域内的潜在引物结合位点。为了提高测序成功率，eOST包括一个简单的动态折叠算法，以自动计算自由能并预测模板内八聚体结合位点附近的二级结构。发现几个参数是重要的，包括碱基质量阈值、模板序列片段的窗口大小和阈值Δ G值。OST与eOST软件相结合，可用于对短DNA片段进行测序，或用于大规模基因组DNA测序的最后组装阶段。
Octamer sequencing technology (OST) is a primer-directed sequencing strategy in which an individual octamer primer is selected from a pre-synthesized octamer primer library and used to sequence a DNA fragment. However, selecting candidate primers from such a library is time consuming and can be a bottleneck in the sequencing process. To accelerate the sequencing process and to obtain high quality sequencing data, a computer program, electronic OST or eOST, was developed to automatically identify candidate primers from an octamer primer library. eOST integrates the base calling software PHRED to provide a quality assessment for target sequences and identifies potential primer binding sites located within a high quality target region. To increase the sequencing success rate, eOST includes a simple dynamic folding algorithm to automatically calculate the free energy and predict the secondary structure within the template in the vicinity of the octamer-binding site. Several parameters were found to be important, including base quality threshold, the window size of the template sequence segment, and the thresholdΔGvalue. OST, coupled with the eOST software, can be used to sequence short DNA fragments or in the finishing assembly stage of large-scale sequencing of genomic DNA.