Li P, Kupfer K C, Davies C J, Burbee D, Evans G A, Garner H R
McDermott Center for Human Growth and Development, The University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Boulevard, Dallas, Texas 75235-8591, USA.
Genomics. 1997 Mar 15;40(3):476-85. doi: 10.1006/geno.1996.4560.
PRIMO is a computer program that designs walking primers for large-scale DNA sequencing projects. Oligonucleotide primers are predicted automatically, using quality information associated with each base call, eliminating the need for manually viewing the sequence traces or inspecting contig assemblies to determine appropriate locations for primer design. This allows PRIMO to run in batch mode on an arbitrarily large number of templates. For shotgun sequencing, PRIMO reads assembled sequence contigs with corresponding base quality statistics and automatically designs walking primers as needed to extend and join contigs, or improve their overall quality. In the opposite extreme of single-pass or completely directed sequencing, PRIMO reads the unassembled sequence for each template and designs walking primers for extending each read. If the base-calling software does not provide base quality statistics, PRIMO assigns its own measure of base quality determined by the shapes of individual peaks in the trace data for each template. In this way, PRIMO can be used in the finishing stages of a shotgun sequencing project, in sequencing by directed primer walking, or in some intermediate strategy. The code is written in ANSI C and maintained in two versions: one for the Macintosh and the other for UNIX.
PRIMO是一个计算机程序，用于为大规模DNA测序项目设计步移引物。利用与每个碱基识别相关的质量信息自动预测寡核苷酸引物，无需人工查看序列图谱或检查重叠群组装情况来确定引物设计的合适位置。这使得PRIMO能够在任意数量的模板上以批处理模式运行。对于鸟枪法测序，PRIMO读取带有相应碱基质量统计信息的组装序列重叠群，并根据需要自动设计步移引物以延伸和连接重叠群，或提高其整体质量。在单通道或完全定向测序的相反极端情况下，PRIMO读取每个模板的未组装序列，并设计步移引物以延伸每个读段。如果碱基识别软件不提供碱基质量统计信息，PRIMO会根据每个模板的痕量数据中各个峰的形状自行确定碱基质量的度量。通过这种方式，PRIMO可用于鸟枪法测序项目的完成阶段、定向引物步移测序或某些中间策略。该代码用ANSI C编写，并维护有两个版本：一个用于Macintosh，另一个用于UNIX。
