Haas S, Vingron M, Poustka A, Wiemann S
Department of Molecular Genome Analysis and Department of Theoretical Bioinformatics,Deutsches Krebsforschungszentrum, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.
Nucleic Acids Res. 1998 Jun 15;26(12):3006-12. doi: 10.1093/nar/26.12.3006.
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 fully 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.
我们开发了PRIDE，这是一个引物设计程序，可在单个重叠群或整个测序项目中自动设计引物，以延伸已知序列并双链化单链区域。该程序完全集成到Staden软件包（GAP4）中，并可通过图形用户界面访问。PRIDE使用基于模糊逻辑的系统来计算引物质量。通过使用后缀树来存储产生的大量数据，提高了PRIDE的计算性能。在基因组模板、cDNA和包含重复元件的序列上设计了一组由110个测序引物和11对PCR引物组成的测试集，以分析PRIDE的成功率。PRIDE的高性能，加上其对用户交互的最低要求和快速算法，使得该程序对于大规模引物设计非常有用，特别是在大型测序项目中。
