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.
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.
Authors: Junkang Rong; John E Bowers; Stefan R Schulze; Vijay N Waghmare; Carl J Rogers; Gary J Pierce; Hua Zhang; James C Estill; Andrew H Paterson Journal: Genome Res Date: 2005-08-18 Impact factor: 9.043
Authors: Junkang Rong; F Alex Feltus; Vijay N Waghmare; Gary J Pierce; Peng W Chee; Xavier Draye; Yehoshua Saranga; Robert J Wright; Thea A Wilkins; O Lloyd May; C Wayne Smith; John R Gannaway; Jonathan F Wendel; Andrew H Paterson Journal: Genetics Date: 2007-06-11 Impact factor: 4.562