Phylogenetic reconstruction from non-genomic data
Phylogenetic reconstruction from non-genomic data
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DOI：
10.1093/bioinformatics/btl307
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发表时间：
2007-01-15
期刊：
影响因子：
5.8
通讯作者：
Valiente, Gabriel
中科院分区：
文献类型：
--
作者：
Clemente, Jose C.;Satou, Kenji;Valiente, Gabriel
动机：最近的结果与水平基因转移表明，系统发育重建不能决定性地确定从序列数据，导致从基于DNA或蛋白质序列的多态性信息的方法，以了解完整的生物过程的演变的研究。越来越多的可用信息的代谢途径的几个物种，使其更大的相关性，以了解这些途径之间的相似性和差异。然后，这些相似性可以用来推断系统发育树不完全基于序列data.Results，因此避免了前面提到的problems.Results：在这篇文章中，我们提出了一种方法来评估几种生物体的代谢途径的结构相似性。我们的算法的工作原理，使用三种可能的酶的相似性措施（层次，信息含量，基因本体），和两个聚类方法（相邻连接，未加权对组的方法与算术平均值）之一，以产生一个系统发育树在Newick和图形格式。实现我们的算法的Web服务器进行了优化，在线性时间内回答查询。
Motivation: Recent results related to horizontal gene transfer suggest that phylogenetic reconstruction cannot be determined conclusively from sequence data, resulting in a shift from approaches based on polymorphism information in DNA or protein sequence to studies aimed at understanding the evolution of complete biological processes. The increasing amount of available information on metabolic pathways for several species makes it of greater relevance to understand the similarities and differences among such pathways. These similarities can then be used to infer phylogenetic trees not based exclusively in sequence data, therefore avoiding the previously mentioned problems.Results: In this article, we present a method to assess the structural similarity of metabolic pathways for several organisms. Our algorithms work by using one of the three possible enzyme similarity measures (hierarchical, information content, gene ontology), and one of the two clustering methods (neighbor-joining, unweighted pair group method with arithmetic mean), to produce a phylogenetic tree both in Newick and graphic format. The web server implementing our algorithms is optimized to answer queries in linear time.