Stenberg Johan, Dahl Fredrik, Landegren Ulf, Nilsson Mats
Department of Genetics and Pathology, Rudbeck Laboratory Se-751 85, Uppsala, Sweden.
Nucleic Acids Res. 2005 Apr 28;33(8):e72. doi: 10.1093/nar/gni071.
We describe PieceMaker, a software tool for the design of applications of selector probes-oligonucleotide probes that direct circularization of target nucleic acid molecules. Such probes can be combined in parallel to circularize a selection of fragments from restriction digested total genomic DNA. These fragments can then be amplified in a single PCR using a common primer pair, yielding substrates for subsequent analyses, such as parallel genotyping or sequencing. However, designing multiplex selector assays is a laborious task. The PieceMaker program alleviates this problem by selecting restriction enzymes to generate suitable fragments for selection, and generating the output data required to design the selector probes.
我们介绍了PieceMaker，这是一种用于设计选择探针（即能引导靶核酸分子环化的寡核苷酸探针）应用的软件工具。此类探针可并行组合，以使限制性消化的全基因组DNA中的一组片段环化。然后，这些片段可使用一对通用引物在单一聚合酶链式反应（PCR）中进行扩增，从而产生用于后续分析（如并行基因分型或测序）的底物。然而，设计多重选择分析是一项艰巨的任务。PieceMaker程序通过选择限制性内切酶以生成适合选择的片段，并生成设计选择探针所需的输出数据，从而缓解了这一问题。
