Discovery of functional genomic motifs in viruses with ViReMa-a Virus Recombination Mapper-for analysis of next-generation sequencing data.
Discovery of functional genomic motifs in viruses with ViReMa-a Virus Recombination Mapper-for analysis of next-generation sequencing data.
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DOI：
10.1093/nar/gkt916
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发表时间：
2014-01
影响因子：
14.9
通讯作者：
Johnson JE
中科院分区：
文献类型：
--
作者：
Routh A;Johnson JE
我们开发了一种名为ViReMa（病毒扩增映射器）的算法，为使用下一代测序数据快速，灵敏和核苷酸分辨率检测病毒基因组中的重组连接提供了一个通用平台。ViReMa不是映射预定义长度和位置的读段，而是动态生成移动读段。ViReMa最初尝试使用基于Bowtie种子的比对将读段的5′端与参考基因组进行比对。然后通过提取读段3′端的任何未对齐核苷酸或通过从读段修剪第一个核苷酸来制备新的读段。这迭代地继续，直到读取的所有部分被映射或修剪。利用多个参考基因组，可以检测病毒与宿主或病毒间的重组。ViReMa还能够在单个读段内检测插入和置换事件以及多个重组连接。通过绘制鸡群病毒基因组中重组事件的分布，我们证明了这些信息可以用来发现位于病毒基因组保守区域的从头功能基序。
We developed an algorithm named ViReMa (Viral-Recombination-Mapper) to provide a versatile platform for rapid, sensitive and nucleotide-resolution detection of recombination junctions in viral genomes using next-generation sequencing data. Rather than mapping read segments of pre-defined lengths and positions, ViReMa dynamically generates moving read segments. ViReMa initially attempts to align the 5′ end of a read to the reference genome(s) with the Bowtie seed-based alignment. A new read segment is then made by either extracting any unaligned nucleotides at the 3′ end of the read or by trimming the first nucleotide from the read. This continues iteratively until all portions of the read are either mapped or trimmed. With multiple reference genomes, it is possible to detect virus-to-host or inter-virus recombination. ViReMa is also capable of detecting insertion and substitution events and multiple recombination junctions within a single read. By mapping the distribution of recombination events in the genome of flock house virus, we demonstrate that this information can be used to discover de novo functional motifs located in conserved regions of the viral genome.
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DOI：
10.3390/v1030895
发表时间：
2009-12
期刊：
Viruses
影响因子：
--
作者：
Pathak KB;Nagy PD
通讯作者：
Nagy PD
影响因子：
3.7
作者：
Jovel J;Schneemann A
通讯作者：
Schneemann A
影响因子：
5.4
作者：
BALL, LA;LI, Y
通讯作者：
LI, Y
DOI：
10.1073/pnas.1116168109
发表时间：
2012-02-07
影响因子：
11.1
作者：
Routh, Andrew;Domitrovic, Tatiana;Johnson, John E.
通讯作者：
Johnson, John E.
影响因子：
5
作者：
Rosskopf, John J.;Upton, John H., III;Rodarte, Lizette;Romero, Tammy A.;Leung, Ming-Ying;Taufer, Michela;Johnson, Kyle L.
通讯作者：
Johnson, Kyle L.