Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences
Sister-Scanning: a Monte Carlo procedure for assessing signals in recombinant sequences
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DOI：
10.1093/bioinformatics/16.7.573
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发表时间：
2000-07-01
期刊：
影响因子：
5.8
通讯作者：
Gibbs, AJ
中科院分区：
文献类型：
--
作者：
Gibbs, MJ;Armstrong, JS;Gibbs, AJ
动机：设计一种方法，与现有方法不同，它直接测量重组导致的基因序列中系统发育信号的变化，测试信号变化的重要性，并区分误导信号。结果：我们开发了一种方法，我们称之为‘姐妹扫描’，用于评估发生在四个核苷酸序列之间的不同同一性模式中的系统发育和组成信号。对窗口内的所有列(位置)进行蒙特卡罗随机化，并且对于四个实序列或具有也随机化的异常值的三个实序列获得Z分数。使用烟草病毒和黄体病毒序列证明了该方法的有效性。在这两个数据集中区分了相互矛盾的系统发育信号，以及不包含明确信号或与成分相似相关的潜在误导性信号的序列区域。在烟草病毒数据集中，相互矛盾的系统发育信号是通过编码长达一千碱基的序列来分离的，这些序列不包含明确的信号。我们使用姊妹扫描对这一数据集的重新分析也产生了我们已知的第一个证据，即病毒依赖RNA的RNA聚合酶基因中存在物种间重组位点，以及三个密码子位置的异常保守模式的证据。
Motivation: To devise a method that, unlike available methods, directly measures variations in phylogenetic signals in gene sequences that result from recombination, tests the significance of the signal variations and distinguishes misleading signals.Results: We have developed a method, that we call 'sister-scanning', for assessing phylogenetic and compositional signals in the various patterns of identity that occur between four nucleotide sequences. A Monte Carlo randomization is done for all columns (positions) within a window and Z-scores are obtained for four real sequences or three real sequences with an outlier that is also randomized. The usefulness of the approach is demonstrated using tobamovirus and luteovirus sequences. Contradictory phylogenetic signals were distinguished in both datasets, as were regions of sequence that contained no clear signal or potentially misleading signals related to compositional similarities. In the tobamovirus dataset, contradictory phylogenetic signals were separated by coding sequences up to a kilobase long that contained no clear signal. Our re-analysis of this dataset using sister-scanning also yielded the first evidence known to us of an interspecies recombination site within a viral RNA-dependent RNA polymerase gene together with evidence of an unusual pattern of conservation in the three codon positions.