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CaptureProbe: a java tool for designing probes for capture Hi-C applications.
Ma, Yun-Fei; Adeola, Adeniyi C; Sun, Yan-Bo; Xie, Hai-Bing; Zhang, Ya-Ping.
Afiliación
  • Ma YF; State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
  • Adeola AC; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China.
  • Sun YB; University of Chinese Academy of Sciences, Beijing 100049, China.
  • Xie HB; State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
  • Zhang YP; State Key Laboratory of Genetic Resources and Evolution, and Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
Zool Res ; 41(1): 94-96, 2020 01 18.
Article en En | MEDLINE | ID: mdl-31840950
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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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Sondas de ADN / Cromosomas / Genómica Límite: Animals / Humans Idioma: En Revista: Zool Res Año: 2020 Tipo del documento: Article País de afiliación: China Pais de publicación: China
Texto completo
Añadir a Mi BVS
Imprimir
XML
PubMed Links
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Texto completo: 1 Colección: 01-internacional Base de datos: MEDLINE Asunto principal: Programas Informáticos / Sondas de ADN / Cromosomas / Genómica Límite: Animals / Humans Idioma: En Revista: Zool Res Año: 2020 Tipo del documento: Article País de afiliación: China Pais de publicación: China