Hillier L, Green P
Genetics Department, Washington University School of Medicine, St. Louis, Missouri 63110.
PCR Methods Appl. 1991 Nov;1(2):124-8. doi: 10.1101/gr.1.2.124.
OSP (Oligonucleotide Selection Program) selects oligonucleotide primers for DNA sequencing and the polymerase chain reaction (PCR). The user can specify (or use default) constraints for primer and amplified product lengths, %(G+C), (absolute or relative) melting temperatures, and primer 3' nucleotides. To help minimize nonspecific priming and primer secondary structure, OSP screens candidate primer sequences, using user-specifiable cutoffs, against potential base-pairing with a variety of sequences present in the reaction, including the primer itself, the other primer (for PCR), the amplified product, and any other sequences desired (e.g., repetitive element sequences in genomic templates, vector sequence in cloned templates, or other primer pair sequences in multiplexed PCR reactions). Base-pairing involving the primer 3' end is considered separately from base-pairing involving internal sequences. Primers meeting all constraints are ranked by a "combined score," a user-definable weighted sum of any of the above parameters. OSP is being routinely and extensively used to select sequencing primers for the Caenorhabditis elegans genome sequencing project and human genomic PCR primer pairs for the Washington University Genome Center mapping project, with success rates exceeding 96% and 81%, respectively. It is available for research purposes from the authors, at no cost, in both text output and interactive graphics (X windows) versions.
OSP（寡核苷酸选择程序）为DNA测序和聚合酶链反应（PCR）选择寡核苷酸引物。用户可以指定（或使用默认值）引物和扩增产物长度、%（G+C）、（绝对或相对）解链温度以及引物3'端核苷酸的限制条件。为了尽量减少非特异性引物结合和引物二级结构，OSP使用用户可指定的临界值，针对与反应中存在的各种序列（包括引物自身、另一条引物（用于PCR）、扩增产物以及任何其他所需序列，如基因组模板中的重复元件序列、克隆模板中的载体序列或多重PCR反应中的其他引物对序列）的潜在碱基配对，对候选引物序列进行筛选。涉及引物3'端的碱基配对与涉及内部序列的碱基配对分开考虑。符合所有限制条件的引物按“综合得分”排序，综合得分是上述任何参数的用户可定义加权和。OSP被常规且广泛地用于为秀丽隐杆线虫基因组测序项目选择测序引物，以及为华盛顿大学基因组中心作图项目选择人类基因组PCR引物对，成功率分别超过96%和81%。作者以文本输出和交互式图形（X窗口）版本两种形式免费提供该程序供研究使用。
