Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
Nucleic Acids Res. 2014 Jan;42(2):e11. doi: 10.1093/nar/gkt916. Epub 2013 Oct 16.
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.
我们开发了一种名为 ViReMa（病毒重组映射器）的算法，为使用下一代测序数据在病毒基因组中快速、敏感且核苷酸分辨率检测重组连接点提供了一个通用的平台。ViReMa 不是映射具有预定义长度和位置的读取段，而是动态生成移动的读取段。ViReMa 最初尝试使用 Bowtie 基于种子的对齐将读取的 5' 端与参考基因组（多个）对齐。然后，通过从读取的 3' 端提取任何未对齐的核苷酸，或者从读取的第一个核苷酸进行修剪，来创建新的读取段。这会一直迭代，直到读取的所有部分都被映射或修剪。对于多个参考基因组，可以检测病毒到宿主或病毒之间的重组。ViReMa 还能够检测单个读取内的插入和替换事件以及多个重组连接点。通过映射 flock house 病毒基因组中重组事件的分布，我们证明了该信息可用于发现位于病毒基因组保守区域内的新功能基序。
