A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.
A configuration space of homologous proteins conserving mutual information and allowing a phylogeny inference based on pair-wise Z-score probabilities.
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DOI：
10.1186/1471-2105-6-49
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发表时间：
2005-03-10
影响因子：
3
通讯作者：
Maréchal E
中科院分区：
文献类型：
--
作者：
Bastien O;Ortet P;Roy S;Maréchal E
重建分子同源性的流行方法是基于多序列比对，其中数据的添加或删除可能会改变所得的树拓扑结构。我们一直在寻求一种同源蛋白质的表示，它将保存成对序列比对的信息，尊重Z分数的概率特性（应用于成对比较的蒙特卡罗方法），并成为一致和稳定的系统发育重建的新方法的基础。我们已经建立了一个空间表示的蛋白质序列使用粒子物理学（配置空间）的概念，并尊重一个框架的约束推导出成对的比对得分属性在信息论。所获得的同源蛋白质（CSHP）的配置空间允许表示的真实的和改组序列，并因此表达的TULIP定理的Z-得分概率。基于CSHP，我们提出了一种基于Z-分数的遗传重建。推导的树，称为TULIP树，与基于多重比对的树一致。此外，TULIP树的重建方法提供了一个解决方案，为一些以前报道的不一致的结果，如apicomplexan烯醇化酶基因。CSHP是一个统一的模型，它以物理模型保存能量的方式保存蛋白质之间的互信息。应用包括重建进化一致和强大的树，其拓扑结构是基于一个空间表示，添加或删除序列后不重新排序。CSHP及其分配的系统发育拓扑结构，提供了一个强大的和易于更新的表示大规模成对的基因组比较的基础上Z分数计算。
Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of homologous proteins that would conserve the information of pair-wise sequence alignments, respect probabilistic properties of Z-scores (Monte Carlo methods applied to pair-wise comparisons) and be the basis for a novel method of consistent and stable phylogenetic reconstruction. We have built up a spatial representation of protein sequences using concepts from particle physics (configuration space) and respecting a frame of constraints deduced from pair-wise alignment score properties in information theory. The obtained configuration space of homologous proteins (CSHP) allows the representation of real and shuffled sequences, and thereupon an expression of the TULIP theorem for Z-score probabilities. Based on the CSHP, we propose a phylogeny reconstruction using Z-scores. Deduced trees, called TULIP trees, are consistent with multiple-alignment based trees. Furthermore, the TULIP tree reconstruction method provides a solution for some previously reported incongruent results, such as the apicomplexan enolase phylogeny. The CSHP is a unified model that conserves mutual information between proteins in the way physical models conserve energy. Applications include the reconstruction of evolutionary consistent and robust trees, the topology of which is based on a spatial representation that is not reordered after addition or removal of sequences. The CSHP and its assigned phylogenetic topology, provide a powerful and easily updated representation for massive pair-wise genome comparisons based on Z-score computations.
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影响因子：
56.9
作者：
FITCH, WM;MARGOLIASH, E
通讯作者：
MARGOLIASH, E
影响因子：
56.9
作者：
DOOLITTLE, RF
通讯作者：
DOOLITTLE, RF
影响因子：
3.9
作者：
ARNHEIM N;STELLER R
通讯作者：
STELLER R
影响因子：
4.8
作者：
Dzierszinski, F;Popescu, O;Tomavo, S
通讯作者：
Tomavo, S
DOI：
10.1016/s0097-8485(01)00074-2
发表时间：
2001-07-01
期刊：
COMPUTERS & CHEMISTRY
影响因子：
--
作者：
Bacro, JN;Comet, JP
通讯作者：
Comet, JP