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首页> 外文期刊>Journal of Bioinformatics and Computational Biology >Reconstructing protein and gene phylogenies using reconciliation and soft-clustering
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Reconstructing protein and gene phylogenies using reconciliation and soft-clustering

机译：使用和解和软聚类重建蛋白质和基因文学

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The architecture of eukaryotic coding genes allows the production of several different protein isoforms by genes. Current gene phylogeny reconstruction methods make use of a single protein product per gene, ignoring information on alternative protein isoforms. These methods often lead to inaccurate gene tree reconstructions that require to be corrected before phylogenetic analyses. Here, we propose a new approach for the reconstruction of gene trees and protein trees accounting for alternative protein isoforms. We extend the concept of reconciliation to protein trees, and we define a new reconciliation problem called MINDRGT that consists in finding a gene tree that minimizes a double reconciliation cost with a given protein tree and a given species tree. We define a second problem called MINDRPGT that consists in finding a protein supertree and a gene tree minimizing a double reconciliation cost, given a species tree and a set of protein subtrees. We propose a shift from the traditional view of protein ortholog groups as hard-clusters to soft-clusters and we study the MINDRPGT problem under this assumption. We provide algorithmic exact and heuristic solutions for versions of the problems, and we present the results of applications on protein and gene trees from the Ensembl database. The implementations of the methods are available at https://github.com/UdeS-CoBIUS/Protein2GeneTree and https://github.com/UdeS-CoBIUS/SuperProteinTree.
机译：真核编码基因的结构允许通过基因产生几种不同的蛋白质同种型。目前基因的系统发生重建方法每种基因使用单一蛋白质产品，忽略替代蛋白质同种型的信息。这些方法通常导致需要在系统发育分析之前需要校正的基因树重建。在这里，我们提出了一种重建基因树木和蛋白质树的新方法，占替代蛋白质同种型。我们将和解对蛋白质树的概念扩展，我们定义了一个名为MindRGT的新的和解问题，该问题包括找到一种基因树，其用给定的蛋白树和给定的物种树尽量减少双重和解成本。我们定义了一个称为MindRPGT的第二个问题，该术语包括找到蛋白质超级和基因树，最小化双重和解成本，给定物种树和一组蛋白质子树。我们提出了从蛋白质原子群的传统观点转变为柔软簇的硬簇，我们在这个假设下研究了MindRPGT问题。我们为问题的版本提供算法精确和启发式解决方案，我们从Ensembl数据库中介绍了蛋白质和基因树上的应用结果。这些方法的实现可在https://github.com/udes-cobius/pricein2genetree和https://github.com/udes-cobius/superproteintree。

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