title: Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice.
abstract: BACKGROUND
  The identification of chromosomal homology will shed light on such mysteries of genome evolution as DNA duplication, rearrangement and loss. Several approaches have been developed to detect chromosomal homology based on gene synteny or colinearity. However, the previously reported implementations lack statistical inferences which are essential to reveal actual homologies.
  
  
  RESULTS
  In this study, we present a statistical approach to detect homologous chromosomal segments based on gene colinearity. We implement this approach in a software package ColinearScan to detect putative colinear regions using a dynamic programming algorithm. Statistical models are proposed to estimate proper parameter values and evaluate the significance of putative homologous regions. Statistical inference, high computational efficiency and flexibility of input data type are three key features of our approach.
  
  
  CONCLUSIONS
  We apply ColinearScan to the Arabidopsis and rice genomes to detect duplicated regions within each species and homologous fragments between these two species. We find many more homologous chromosomal segments in the rice genome than previously reported. We also find many small colinear segments between rice and Arabidopsis genomes.
authors.affiliation: College of Life Sciences, National Laboratory of Plant Genetic Engineering and Protein Engineering, Center of Bioinformatics, Peking University, Beijing 100871, China. wangxy@mail.cbi.pku.edu.cn
authors.forename: Xiyin
authors.initials: X
authors.lastname: Wang
authors.forename: Xiaoli
authors.initials: X
authors.lastname: Shi
authors.forename: Zhe
authors.initials: Z
authors.lastname: Li
authors.forename: Qihui
authors.initials: Q
authors.lastname: Zhu
authors.forename: Lei
authors.initials: L
authors.lastname: Kong
authors.forename: Wen
authors.initials: W
authors.lastname: Tang
authors.forename: Song
authors.initials: S
authors.lastname: Ge
authors.forename: Jingchu
authors.initials: J
authors.lastname: Luo
mesh_terms: D000465:Algorithms; D017360:Arabidopsis / Q000235:genetics*; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D032461:Chromosomes, Plant / Q000235:genetics*; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D018745:Genome, Plant / Q000235:genetics*; D008957:Models, Genetic; D015233:Models, Statistical; D008969:Molecular Sequence Data; D005810:Multigene Family / Q000235:genetics*; D012275:Oryza / Q000235:genetics*; D012689:Sequence Homology, Nucleic Acid; D026801:Synteny / Q000235:genetics*