Fast identification and statistical evaluation of segmental homologies in comparative maps

被引:61
作者
Calabrese, Peter P. [3 ]
Chakravarty, Sugata [2 ]
Vision, Todd J. [1 ]
机构
[1] Univ N Carolina, Dept Biol, Chapel Hill, NC 27599 USA
[2] Univ N Carolina, Dept Operat Res, Chapel Hill, NC 27599 USA
[3] Univ So Calif, Dept Math, Los Angeles, CA 90089 USA
关键词
homology; comparative maps; synteny; genome evolution;
D O I
10.1093/bioinformatics/btg1008
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Motivation: Chromosomal segments that share common ancestry, either through genomic duplication or species divergence, are said to be segmental homologs of one another. Their identification allows researchers to leverage knowledge of model organisms for use in other systems and is of value for studies of genome evolution. However, identification and statistical evaluation of segmental homologies can be a challenge when the segments are highly diverged. Results: We describe a flexible dynamic programming algorithm for the identification of segments having multiple homologous features. We model the probability of observing putative segmental homologies by chance and incorporate our findings into the parameterization of the algorithm and the statistical evaluation of its output. Combined, these findings allow segmental homologies to be identified in comparisons within and between genomic maps in a rigorous, rapid, and automated fashion.
引用
收藏
页码:i74 / i80
页数:7
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