Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
Bioinformatics. 2011 Mar 1;27(5):720-2. doi: 10.1093/bioinformatics/btq722. Epub 2011 Jan 17.
Retroviral integration has been implicated in several biomedical applications, including identification of cancer-associated genes and malignant transformation in gene therapy clinical trials. We introduce an efficient and scalable method for fast identification of viral vector integration sites from long read high-throughput sequencing. Individual sequence reads are masked to remove non-genomic sequence, aligned to the host genome and assembled into contiguous fragments used to pinpoint the position of integration.
The method is implemented in a publicly accessible web server platform, SeqMap 2.0, containing analysis tools and both private and shared lab workspaces that facilitate collaboration among researchers. Available at http://seqmap.compbio.iupui.edu/.
逆转录病毒整合已涉及到几种生物医学应用，包括鉴定癌症相关基因和基因治疗临床试验中的恶性转化。我们引入了一种从高通量测序的长读序列中快速鉴定病毒载体整合位点的高效且可扩展的方法。单独的序列读段被屏蔽以去除非基因组序列，然后与宿主基因组对齐并组装成连续片段，用于精确定位整合位置。
该方法在一个可公开访问的网络服务器平台 SeqMap 2.0 中实现，该平台包含分析工具以及私有和共享的实验室工作区，方便研究人员之间的协作。可在 http://seqmap.compbio.iupui.edu/ 获得。
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