ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.
ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution.
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DOI：
10.1093/bioinformatics/btt011
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发表时间：
2013-03-01
期刊：
影响因子：
--
通讯作者：
Chan TF
中科院分区：
文献类型：
--
作者：
Li JW;Wan R;Yu CS;Co NN;Wong N;Chan TF
摘要：病毒感染引起的插入性突变是癌症发生的重要致病风险。尽管出现了高通量测序，病毒整合位点和表达的病毒融合事件的发现仍然有限。在这里，我们提出了ViralFusionSeq (VFS)，它结合了软剪切信息、读对分析和靶向从头组装来发现和注释病毒与人的融合。使用VFS进行RNA-Seq实验、模拟DNA-Seq实验和重新分析已发表的DNA-Seq数据集。实验结果表明，VFS具有较高的灵敏度和精度。可用性：VFS在GPL版本3下发布在http://hkbic.cuhk.edu.hk/software/viralfusionseq联系：tf.chan@cuhk.edu.hk补充信息：补充数据可在Bioinformatics Online上获得
Summary: Insertional mutagenesis from virus infection is an important pathogenic risk for the development of cancer. Despite the advent of high-throughput sequencing, discovery of viral integration sites and expressed viral fusion events are still limited. Here, we present ViralFusionSeq (VFS), which combines soft-clipping information, read-pair analysis and targeted de novo assembly to discover and annotate viral–human fusions. VFS was used in an RNA-Seq experiment, simulated DNA-Seq experiment and re-analysis of published DNA-Seq datasets. Our experiments demonstrated that VFS is both sensitive and highly accurate. Availability: VFS is distributed under GPL version 3 at http://hkbic.cuhk.edu.hk/software/viralfusionseq Contact: tf.chan@cuhk.edu.hk Supplementary information: Supplementary data are available at Bioinformatics Online
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作者：
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DOI：
10.1093/bioinformatics/btp698
发表时间：
2010-03-01
期刊：
Bioinformatics (Oxford, England)
影响因子：
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作者：
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通讯作者：
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