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对于SNP的基因型分析，该程序设计了引物旁侧突变，如SNPs、DIPs（/插入多态性）和MNPs（多核苷酸多态性）。
评估预设计的引物和探针
PrimerPlex可以使用预先设计的经过验证的oligos来构建复用集。在为每个序列了oligo之后，对它们的属性进行分析，并为发现的任何偏差提醒用户。对于预先设计的oligos不可用的序列，PrimerPlex设计它们，检查它们是否复用，并强调兼容性问题。然后用户可以决定接受这个设计或者创建一个单的池。这个功能在用户的手中提供了完全的控制。
"I used Beacon Designer for TaqMan assay design as well as designing probes from previously designed primers. I was able to navigate the program fairly easily so I would give high marks for ease of use. I also very much liked the interface with BLAST for potential regions of cross homology. Overall the program seemed to do a good job of providing template specific primers and probes." -Dr. Ryan Troyer, Colorado State University, United States.
Razieh Fatehi, Sharifeh Khosravi, Maryam Abedi, Rasoul Salehi, Yousof Gheisari.
Journal of Research in Medical Sciences. 2017; Sep 26;22:102. doi: 10.4103/jrms.JRMS_136_17.
"I used Beacon Designer™ for designing new assays. I found it simple to use and it met my expectations well. The performance was great and I obtained good results. The design options were exhaustive, saving my time." -Meritxell Espino Guarch, IDIBELL-CGMM, Spain.
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