标题： 无序列比对的分子进化随机替换-插入-删除模型 显示英文标题

标题： Random Substitution-Insertion-Deletion (RSID) Model of Molecular Evolution with Alignment-free Parameter Estimation

摘要： 我们提出了一种全面的新框架，用于处理分子进化中生物准确的模型。 该模型提供了一个系统框架，用于研究实现异质速率、阅读框保守性、插入和删除的不同速率、可自定义的概率和类型的替换、插入和删除，以及相邻依赖性的分子进化模型。 我们以无限状态马尔可夫链的形式陈述该模型，以最大化在模型分析中有用的适用定理数量。 我们利用这些定理开发了一种无需比对的参数估计技术。 这种无需比对的技术避免了许多与依赖比对的估计相关的细微问题。 然后，我们将我们的模型实现应用于以完全无需比对的方式重现张和Gerstein（2003）关于人类核糖体蛋白假基因中插入缺失长度分布的一些观察结果。 显示英文摘要

摘要： We present a comprehensive new framework for handling biologically accurate models of molecular evolution. This model provides a systematic framework for studying models of molecular evolution that implement heterogeneous rates, conservation of reading frame, differing rates of insertion and deletion, customizable parametrization of the probabilities and types of substitutions, insertions, and deletions, as well as neighboring dependencies. We have stated the model in terms of an infinite state Markov chain in order to maximize the number of applicable theorems useful in the analysis of the model. We use such theorems to develop an alignment-free parameter estimation technique. This alignment-free technique circumvents many of the nuanced issues related to alignment-dependent estimation. We then apply an implementation of our model to reproduce (in a completely alignment-free fashion) some observed results of Zhang and Gerstein (2003) regarding indel length distribution in human ribosomal protein pseudogenes.