Primer design for large scale sequencing
Primer design for large scale sequencing
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DOI：
10.1093/nar/26.12.3006
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发表时间：
1998-06-15
影响因子：
14.9
通讯作者：
Wiemann, S
中科院分区：
文献类型：
--
作者：
Haas, S;Vingron, M;Wiemann, S
我们开发了 PRIDE，这是一种引物设计程序，可以自动设计单个重叠群或整个测序项目中的引物，以扩展已知的序列和双链单链区域。该程序被 Bully 集成到 Staden 软件包 (GAP4) 中，并可通过图形用户界面进行访问。 PRIDE 使用基于模糊逻辑的系统来计算底漆质量。通过使用后缀树来存储产生的大量数据，PRIDE 的计算性能得到了增强。针对基因组模板、cDNA 和含有重复元件的序列设计了 110 个测序引物和 11 个 PCR 引物对的测试集，以分析 PRIDE 的成功率。 PRIDE 的高性能，结合其对用户交互的最低要求和快速算法，使该程序可用于大规模引物设计，特别是在大型测序项目中。
We have developed PRIDE, a primer design program that automatically designs primers in single contigs or whole sequencing projects to extend the already known sequence and to double strand single-stranded regions. The program is Bully integrated into the Staden package (GAP4) and accessible with a graphical user interface. PRIDE uses a fuzzy logic-based system to calculate primer qualities. The computational performance of PRIDE is enhanced by using suffix trees to store the huge amount of data being produced. A test set of 110 sequencing primers and 11 PCR primer pairs has been designed on genomic templates, cDNAs and sequences containing repetitive elements to analyze PRIDE's success rate. The high performance of PRIDE, combined with its minimal requirement of user interaction and its fast algorithm, make this program useful for the large scale design of primers, especially in large sequencing projects.