Ma Jian, Ratan Aakrosh, Raney Brian J, Suh Bernard B, Zhang Louxin, Miller Webb, Haussler David
Center for Biomolecular Science and Engineering, University of California, Santa Cruz, CA 95064, USA.
J Comput Biol. 2008 Oct;15(8):1007-27. doi: 10.1089/cmb.2008.0069.
Accurately reconstructing the large-scale gene order in an ancestral genome is a critical step to better understand genome evolution. In this paper, we propose a heuristic algorithm, called DUPCAR, for reconstructing ancestral genomic orders with duplications. The method starts from the order of genes in modern genomes and predicts predecessor and successor relationships in the ancestor. Then a greedy algorithm is used to reconstruct the ancestral orders by connecting genes into contiguous regions based on predicted adjacencies. Computer simulation was used to validate the algorithm. We also applied the method to reconstruct the ancestral chromosome X of placental mammals and the ancestral genomes of the ciliate Paramecium tetraurelia.
准确重建祖先基因组中的大规模基因顺序是更好理解基因组进化的关键一步。在本文中，我们提出了一种启发式算法，称为DUPCAR，用于重建存在重复的祖先基因组顺序。该方法从现代基因组中的基因顺序开始，预测祖先中的前驱和后继关系。然后使用贪婪算法，根据预测的邻接关系将基因连接成连续区域，从而重建祖先顺序。通过计算机模拟对该算法进行了验证。我们还应用该方法重建了胎盘哺乳动物的祖先X染色体以及纤毛虫四膜虫的祖先基因组。
