HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching
HomBlocks: A multiple-alignment construction pipeline for organelle phylogenomics based on locally collinear block searching
复制标题
HomBlocks：基于局部共线块搜索的细胞器系统基因组学多比对构建流程
DOI：
10.1016/j.ygeno.2017.08.001
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发表时间：
2018-01-01
期刊：
影响因子：
4.4
通讯作者：
Cao, Min
中科院分区：
文献类型：
--
作者：
Bi, Guiqi;Mao, Yunxiang;Cao, Min
细胞器基因组学分析需要精确构建的多基因比对矩阵连接的预对齐的单基因数据集。对于非生物信息学家来说，手动创建包含数十或数百个同源基因的高质量多基因比对可能需要数天至数周的时间。在这里，我们描述了一个新的和高效的管道，HomBlocks，它使用同源块搜索方法来构建多序列比对。该方法可以在几个小时内自动识别细胞器基因组中的局部共线块，并挖掘遗传信息区域以构建多序列比对。此外，HomBlocks支持无注释的细胞器基因组，并对不同的分类单元数据集进行调整，从而能够包含尽可能多的共同基因。拓扑结构比较的树建立了传统的多基因和HomBlocks比对实施不同的分类单元类别表明，相同的效率，可以实现HomBlocks时，使用传统的方法。Homblocks的可用性使得非生物信息学家更容易获得细胞器系统发育分析，从而有希望在细胞器基因组水平上更好地理解基因组关系。可用性和实现：HomBlocks是用Perl实现的，并得到类Unix操作系统的支持，包括Linux和macOS。Perl源代码可以从https://github.com/fenghen360/HomBlocks.git免费下载，文档和教程可以从https：//github.com/fenghen360/HomBlocks获得。
Organelle phylogenomic analysis requires precisely constructed multi-gene alignment matrices concatenated by pre-aligned single gene datasets. For non-bioinformaticians, it can take days to weeks to manually create high-quality multi-gene alignments comprising tens or hundreds of homologous genes. Here, we describe a new and highly efficient pipeline, HomBlocks, which uses a homologous block searching method to construct multiple sequence alignment. This approach can automatically recognize locally collinear blocks among organelle genomes and excavate phylogenetically informative regions to construct multiple sequence alignment in a few hours. In addition, HomBlocks supports organelle genomes without annotation and makes adjustment to different taxon datasets, thereby enabling the inclusion of as many common genes as possible. Topology comparison of trees built by conventional multi-gene and HomBlocks alignments implemented in different taxon categories shows that the same efficiency can be achieved by HomBlocks as when using the traditional method. The availability of Homblocks makes organelle phylogenetic analyses more accessible to non-bioinformaticians, thereby promising to lead to a better understanding of phylogenic relationships at an organelle genome level. Availability and implementation: HomBlocks is implemented in Perl and is supported by Unix-like operative systems, including Linux and macOS. The Perl source code is freely available for download from https://github.com/fenghen360/HomBlocks.git, and documentation and tutorials are available at https://github.com/fenghen360/HomBlocks.