Detecting Coevolution of Functionally Related Proteins for Automated Protein Annotation.
Detecting Coevolution of Functionally Related Proteins for Automated Protein Annotation.
复制标题
检测功能相关蛋白质的共同进化以进行自动蛋白质注释。
DOI：
10.1109/bibe.2010.24
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发表时间：
2010
期刊：
影响因子：
--
通讯作者：
Stormo,GaryD
中科院分区：
文献类型：
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作者：
Kwan,AlanL;Dutcher,SusanK;Stormo,GaryD
基于序列相似性的蛋白质聚类方法将蛋白质组织成相似序列的家族，这一任务仍然是自动化蛋白质表征的关键。然而，许多蛋白质家族无法自动进一步表征，因为对相似序列家族中任何蛋白质的功能知之甚少。我们提出了一种新的系统发育谱比较（PPC）方法，称为协调进化自动蛋白质注释（APACE），该方法可以促进蛋白质的自动表征，而不仅仅是它们与其他类似序列的同源性。我们的方法实现了多物种间相似性评分归一化的新方法，并通过蛋白质与其他不一定具有相似序列的蛋白质的共同进化模式自动表征蛋白质。我们证明我们的方法能够概括最新的，未解决的，复合的深层真核生物系统发育的拓扑结构，并且能够量化尚未解决的分支长度。我们进一步证明，在给定相同的起始数据的情况下，我们的方法能够检测到比现有方法更多的功能相关蛋白。最后，我们证明，我们的方法可以成功地应用于更大的比较基因组问题的情况下，现有的方法往往失败。
Sequence similarity based protein clustering methods organize proteins into families of similar sequences, a task that continues to be critical for automated protein characterization. However, many protein families cannot be automatically characterized further because little is known about the function of any protein in a family of similar sequences. We present a novel phylogenetic profile comparison (PPC) method called Automated Protein Annotation by Coordinate Evolution (APACE) that facilitates the automated characterization of proteins beyond their homology to other similar sequences. Our method implements a new approach for the normalization of similarity scores among multiple species and automates the characterization of proteins by their patterns of co-evolution with other proteins that do not necessarily share a similar sequence. We demonstrate that our method is able to recapitulate the topology of the latest, unresolved, composite deep eukaryotic phylogeny and is able to quantify the as yet unresolved branch lengths. We further demonstrate that our method is able to detect more functionally related proteins, given the same starting data, than existing methods. Finally, we demonstrate that our method can be successfully applied to much larger comparative genomic problem instances where existing methods often fail.