DUPCAR: Reconstructing contiguous ancestral regions with duplications

Jian Ma, Aakrosh Ratan, Brian J. Raney, Bernard B. Suh, Louxin Zhang, Webb Miller, David Haussler

Research output: Contribution to journalArticlepeer-review

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1007-1027
Number of pages21
JournalJournal of Computational Biology
Volume15
Issue number8
DOIs
StatePublished - Oct 1 2008
Externally publishedYes

Keywords

  • Contiguous ancestral region
  • Duplication
  • Gene-order reconstruction
  • Genome rearrangement
  • Isometric reconciliation

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Modeling and Simulation
  • Computational Theory and Mathematics

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