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马云飞, Adeniyi C. Adeola, 孙艳波, 谢海兵, 张亚平. 2020: CaptureProbe: 一款用于开展捕获Hi-C研究的探针设计软件. 动物学研究, 41(1): 94-96. DOI: 10.24272/j.issn.2095-8137.2020.010
引用本文: 马云飞, Adeniyi C. Adeola, 孙艳波, 谢海兵, 张亚平. 2020: CaptureProbe: 一款用于开展捕获Hi-C研究的探针设计软件. 动物学研究, 41(1): 94-96. DOI: 10.24272/j.issn.2095-8137.2020.010
Yun-Fei Ma, Adeniyi C. Adeola, Yan-Bo Sun, Hai-Bing Xie, Ya-Ping Zhang. 2020: CaptureProbe: a java tool for designing probes for capture Hi-C applications. Zoological Research, 41(1): 94-96. DOI: 10.24272/j.issn.2095-8137.2020.010
Citation: Yun-Fei Ma, Adeniyi C. Adeola, Yan-Bo Sun, Hai-Bing Xie, Ya-Ping Zhang. 2020: CaptureProbe: a java tool for designing probes for capture Hi-C applications. Zoological Research, 41(1): 94-96. DOI: 10.24272/j.issn.2095-8137.2020.010

CaptureProbe: 一款用于开展捕获Hi-C研究的探针设计软件

CaptureProbe: a java tool for designing probes for capture Hi-C applications

  • 摘要: 许多与生物表型和疾病相关联的功能元件都位于非编码区,并且通过染色体出环和折叠的方式作用于远端靶基因,使得研究人员难于揭示其参与的遗传调控机制。捕获Hi-C是一项新的染色体构象捕获技术,其原理基于探针与目的遗传区域间的杂交捕获。捕获Hi-C可以实现低成本获取靶位点与基因组上其它位点之间相互作用的高精度图谱。本文中,我们开发了一款用户友好的图形Java软件(CaptureProbe),用于多个靶位点或者靶区段的捕获探针设计。软件提供的多个参数可以实现探针的最优设计。对CaptureProbe设计的探针开展相关测试,结果显示其具有很好的探针设计成功率和探针特异性。因此,该软件可以帮助研究人员开展基因组水平的空间互作研究。CaptureProbe和相关代码的下载地址为:https://sourceforge.net/projects/captureprobe/。

     

    Abstract: Many functional elements associated with traits and diseases are located in non-coding regions and act on distant target genes via chromatin looping and folding, making it difficult for scientists to reveal the genetic regulatory mechanisms. Capture Hi-C is a newly developed chromosome conformation capture technology based on hybridization capture between probes and target genomic regions. It can identify interactions among target loci and all other loci in a genome with low cost and high resolution. Here, we developed CaptureProbe, a user-friendly, graphical Java tool for the design of capture probes across a range of target sites or regions. Numerous parameters helped to achieve and optimize the designed probes. Design testing of CaptureProbe showed high efficiency in the design success ratio of target loci and probe specificity. Hence, this program will help scientists conduct genome spatial interaction research. CaptureProbe and source code are available at https://sourceforge.net/projects/captureprobe/.

     

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