A Heuristic Algorithm for Reconstructing Ancestral Gene Orders with Duplications

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 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 genomes of ciliate Paramecium tetraurelia.

• Type: Conference
• Year: 2007
• Where: RECOMB
• Authors: Jian Ma, Aakrosh Ratan, Louxin Zhang, Webb Miller, David Haussler
• Keywords: Better Understand Genome, Ciliate Paramecium Tetraurelia, Computational Biology, Large-scale Gene Order, RECOMB 2007