RDP4: Detection and analysis of recombination patterns in virus genomes.
RDP4: Detection and analysis of recombination patterns in virus genomes.
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DOI：
10.1093/ve/vev003
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发表时间：
2015
期刊：
影响因子：
5.3
通讯作者：
Muhire B
中科院分区：
文献类型：
--
作者：
Martin DP;Murrell B;Golden M;Khoosal A;Muhire B
RDP4是重组检测程序（RDP）的最新版本，RDP是一种Windows计算机程序，可实现一系列广泛的方法，用于检测和可视化病毒基因组序列比对中的重组，并从病毒基因组序列比对中剥离重组证据。RDP4能够分析两倍多的序列（多达2，500个），这些序列比旧版本的程序可以分析的序列长三倍（高达10 Mb）。因此，RDP4也适用于细菌全基因组序列数据集的分析。RDP4的其他创新包括（1）区分重组和基因组片段重配的能力，（2）重组断点置信区间的估计，（3）各种“重组感知”系统发育树构建和比较工具，（4）新的基于矩阵的可视化工具，用于检查单个重组事件和多个重组事件的总体系统发育影响，以及（5）检测基因排列、编码蛋白质结构、核酸二级结构、核苷酸组成和核苷酸多样性对重组断点模式的影响的新测试。RDP4区别于其他重组检测工具的关键特征是其灵活性。它既可以从命令行界面以全自动模式运行，也可以通过图形丰富的用户界面运行，从而可以详细探索单个重组事件和整体重组模式。
RDP4 is the latest version of recombination detection program (RDP), a Windows computer program that implements an extensive array of methods for detecting and visualising recombination in, and stripping evidence of recombination from, virus genome sequence alignments. RDP4 is capable of analysing twice as many sequences (up to 2,500) that are up to three times longer (up to 10 Mb) than those that could be analysed by older versions of the program. RDP4 is therefore also applicable to the analysis of bacterial full-genome sequence datasets. Other novelties in RDP4 include (1) the capacity to differentiate between recombination and genome segment reassortment, (2) the estimation of recombination breakpoint confidence intervals, (3) a variety of ‘recombination aware’ phylogenetic tree construction and comparison tools, (4) new matrix-based visualisation tools for examining both individual recombination events and the overall phylogenetic impacts of multiple recombination events and (5) new tests to detect the influences of gene arrangements, encoded protein structure, nucleic acid secondary structure, nucleotide composition, and nucleotide diversity on recombination breakpoint patterns. The key feature of RDP4 that differentiates it from other recombination detection tools is its flexibility. It can be run either in fully automated mode from the command line interface or with a graphically rich user interface that enables detailed exploration of both individual recombination events and overall recombination patterns.