Evolutionary Fingerprinting of Genes
Evolutionary Fingerprinting of Genes
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DOI：
10.1093/molbev/msp260
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发表时间：
2010-03-01
影响因子：
10.7
通讯作者：
Frost, Simon D. W.
中科院分区：
文献类型：
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作者：
Pond, Sergei L. Kosakovsky;Scheffler, Konrad;Frost, Simon D. W.
为了验证这一假设，我们开发了一种新的模型，编码序列的进化，使用一般的双变量离散参数化的进化速率。我们表明，这种方法提供了一个更好的拟合数据使用更少的参数比现有的模型。接下来，我们使用该模型将进化指纹表示为概率分布，并提出了一种方法来比较这些分布，这种方法对数据集大小和分歧的变化具有鲁棒性。最后，使用三种快速进化的RNA病毒（HIV-1，丙型肝炎病毒和甲型流感病毒）的序列，我们证明了同一功能组内的基因往往具有相似的进化指纹。我们的框架提供了一个良好的统计基础，有效的推理和比较的进化速率模式在任意集合的基因比对，聚类同源和非同源基因，和生物和功能相关的进化速率的调查。
To test this hypothesis, we develop a novel model of coding sequence evolution that uses a general bivariate discrete parameterization of the evolutionary rates. We show that this approach provides a better fit to the data using a smaller number of parameters than existing models. Next, we use the model to represent evolutionary fingerprints as probability distributions and present a methodology for comparing these distributions in a way that is robust against variations in data set size and divergence. Finally, using sequences of three rapidly evolving RNA viruses (HIV-1, hepatitis C virus, and influenza A virus), we demonstrate that genes within the same functional group tend to have similar evolutionary fingerprints. Our framework provides a sound statistical foundation for efficient inference and comparison of evolutionary rate patterns in arbitrary collections of gene alignments, clustering homologous and nonhomologous genes, and investigation of biological and functional correlates of evolutionary rates.