Phylogenetic reconstruction from transpositions.
Phylogenetic reconstruction from transpositions.
复制标题
DOI：
10.1186/1471-2164-9-s2-s15
复制
发表时间：
2008-09-16
期刊：
影响因子：
4.4
通讯作者：
Tang J
中科院分区：
文献类型：
--
作者：
Yue F;Zhang M;Tang J
由于高通量测序技术的出现和测序成本的降低，许多生物已经被完全测序，它们的大部分基因已经被鉴定出来。因此，将整个基因组表示为基因标识符的有序列表并通过计算手段研究这些实体的重排已成为可能。因此，基因组重排数据作为一种新型的系统发育分析数据越来越受到生物学家和计算机科学家的关注。基因组重排的主要事件包括倒位、转位和倒位。迄今为止，GRAPPA和MGR是最准确的重排系统发育方法，它们都假设反转是唯一的事件。然而，由于计算换位距离的复杂性，当换位占主导地位时，对数据集进行分析非常困难。我们扩展了GRAPPA来处理换位。新方法被命名为GRAPPA-TP，它有两个主要的扩展：一个估计转位距离的启发式方法，一个新的三个基因组的转位中值求解器。尽管GRAPPA-TP使用贪婪方法来计算转位距离，但当基因组相对接近时，它是非常准确的。新的GRAPPA-TP可从。我们使用模拟数据集进行的广泛测试表明，GRAPPA-TP在祖先基因组推断和系统发育重建方面非常准确。模拟结果还表明，模型匹配在基因组重排分析中是至关重要的：模拟包括倒置在内的其他事件的转位是不准确的。
Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become possible to represent whole genomes as ordered lists of gene identifiers and to study the rearrangement of these entities through computational means. As a result, genome rearrangement data has attracted increasing attentions from both biologists and computer scientists as a new type of data for phylogenetic analysis. The main events of genome rearrangements include inversions, transpositions and transversions. To date, GRAPPA and MGR are the most accurate methods for rearrangement phylogeny, both assuming inversion as the only event. However, due to the complexity of computing transposition distance, it is very difficult to analyze datasets when transpositions are dominant. We extend GRAPPA to handle transpositions. The new method is named GRAPPA-TP, with two major extensions: a heuristic method to estimate transposition distance, and a new transposition median solver for three genomes. Although GRAPPA-TP uses a greedy approach to compute the transposition distance, it is very accurate when genomes are relatively close. The new GRAPPA-TP is available from . Our extensive testing using simulated datasets shows that GRAPPA-TP is very accurate in terms of ancestor genome inference and phylogenetic reconstruction. Simulation results also suggest that model match is critical in genome rearrangement analysis: it is not accurate to simulate transpositions with other events including inversions.