Volume 41 Issue 1
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Yun-Fei Ma, Adeniyi C. Adeola, Yan-Bo Sun, Hai-Bing Xie, Ya-Ping Zhang. CaptureProbe: a java tool for designing probes for capture Hi-C applications. Zoological Research, 2020, 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. CaptureProbe: a java tool for designing probes for capture Hi-C applications. Zoological Research, 2020, 41(1): 94-96. doi: 10.24272/j.issn.2095-8137.2020.010

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

doi: 10.24272/j.issn.2095-8137.2020.010
Funds:  the Ministry of Agriculture of China(2016ZX08009003-006);Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences (Large Research Infrastructure Funding);This work was supported by the Ministry of Agriculture of China (2016ZX08009003-006) and Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences (Large Research Infrastructure Funding)
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  • Corresponding author: Hai-Bing Xie,Ya-Ping Zhang
  • Received Date: 2019-11-15
  • Publish Date: 2020-01-18
  • 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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CaptureProbe: a java tool for designing probes for capture Hi-C applications

doi: 10.24272/j.issn.2095-8137.2020.010
Funds:  the Ministry of Agriculture of China(2016ZX08009003-006);Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences (Large Research Infrastructure Funding);This work was supported by the Ministry of Agriculture of China (2016ZX08009003-006) and Animal Branch of the Germplasm Bank of Wild Species, Chinese Academy of Sciences (Large Research Infrastructure Funding)
    Corresponding author: Hai-Bing Xie,Ya-Ping Zhang

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/.

Yun-Fei Ma, Adeniyi C. Adeola, Yan-Bo Sun, Hai-Bing Xie, Ya-Ping Zhang. CaptureProbe: a java tool for designing probes for capture Hi-C applications. Zoological Research, 2020, 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. CaptureProbe: a java tool for designing probes for capture Hi-C applications. Zoological Research, 2020, 41(1): 94-96. doi: 10.24272/j.issn.2095-8137.2020.010
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