HiCapTools：用于靶向染色体构象捕获应用的探针设计和邻近检测的软件套件。
HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications.
机构信息
KTH - Royal Institute of Technology, Science for Life Laboratory, School of Biotechnology, Solna 171?65, Sweden.
出版信息
Bioinformatics. 2018 Feb 15;34(4):675-677. doi: 10.1093/bioinformatics/btx625.
SUMMARY
Folding of eukaryotic genomes within nuclear space enables physical and functional contacts between regions that are otherwise kilobases away in sequence space. Targeted chromosome conformation capture methods (T2C, chi-C and HiCap) are capable of informing genomic contacts for a subset of regions targeted by probes. We here present HiCapTools, a software package that can design sequence capture probes for targeted chromosome capture applications and analyse sequencing output to detect proximities involving targeted fragments. Two probes are designed for each feature while avoiding repeat elements and non-unique regions. The data analysis suite processes alignment files to report genomic proximities for each feature at restriction fragment level and is isoform-aware for gene features. Statistical significance of contact frequencies is evaluated using an empirically derived background distribution. Targeted chromosome conformation capture applications are invaluable for locating target genes of disease-associated variants found by genome-wide association studies. Hence, we believe our software suite will prove to be useful for a wider user base within clinical and functional applications.
AVAILABILITY
https://github.com/sahlenlab/HiCapTools.
CONTACT
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
真核生物基因组在核空间内的折叠使在序列空间中相隔数千碱基的区域能够发生物理和功能接触。靶向染色体构象捕获方法（T2C、chi-C 和 HiCap）能够为探针靶向的一部分区域提供基因组接触信息。我们在此介绍 HiCapTools，这是一个软件包，可用于设计靶向染色体捕获应用的序列捕获探针，并分析测序输出以检测涉及靶向片段的接近度。为每个特征设计两个探针，同时避免重复元件和非独特区域。数据分析套件处理比对文件，以报告每个特征在限制片段水平上的基因组接近度，并且针对基因特征具有异构体意识。使用经验导出的背景分布来评估接触频率的统计学显着性。靶向染色体构象捕获应用对于定位全基因组关联研究中发现的与疾病相关变异的靶基因非常有价值。因此，我们相信我们的软件套件将在临床和功能应用中为更广泛的用户群体提供有用的帮助。
网址
https://github.com/sahlenlab/HiCapTools。
联系人
补充信息
补充数据可在“Bioinformatics”在线获取。
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