Statistical inference of chromosomal homology based on gene colinearity   and applications to Arabidopsis and rice

doi:10.1186/1471-2105-7-447

CORC > 北京大学 > 生命科学学院

	Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice
	Wang, Xiyin ; Shi, Xiaoli ; Li, Zhe ; Zhu, Qihui ; Kong, Lei ; Tang, Wen ; Ge, Song ; Luo, Jingchu
刊名	bmc bioinformatics
	2006
关键词	MONOCOT-DICOT DIVERGENCE GENOME DUPLICATION RECENT POLYPLOIDY ANCIENT EVOLUTION SEQUENCE THALIANA PATTERNS PROGRAMS CEREALS
DOI	10.1186/1471-2105-7-447
英文摘要	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. Conclusion: 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.; http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000241638000001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=8e1609b174ce4e31116a60747a720701 ; Biochemical Research Methods; Biotechnology & Applied Microbiology; Mathematical & Computational Biology; SCI(E); PubMed; 46; ARTICLE; 447; 7
语种	英语
内容类型	期刊论文
源URL	[http://ir.pku.edu.cn/handle/20.500.11897/198665]
专题	生命科学学院
推荐引用方式 GB/T 7714	Wang, Xiyin,Shi, Xiaoli,Li, Zhe,et al. Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice[J]. bmc bioinformatics,2006.
APA	Wang, Xiyin.,Shi, Xiaoli.,Li, Zhe.,Zhu, Qihui.,Kong, Lei.,...&Luo, Jingchu.(2006).Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice.bmc bioinformatics.
MLA	Wang, Xiyin,et al."Statistical inference of chromosomal homology based on gene colinearity and applications to Arabidopsis and rice".bmc bioinformatics (2006).