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The availability of the complete chicken genome sequence provides an unprecedented opportunity to study the global genome organization at the sequence level. Delineating compositionally homogeneous G + C domains in DNA sequences can provide much insight into the understanding of the organization and biological functions of the chicken genome. | FEBS Journal Isochore structures in the chicken genome Feng Gao and Chun-Ting Zhang Department of Physics Tianjin University China Keywords compositional homogeneity compositional segmentation Gallus gallus isochores windowless technique Correspondence C.-T. Zhang Department of Physics Tianjin University Tianjin 300072 China Fax 86 22 27402697 Tel 86 22 27402987 E-mail ctzhang@tju.edu.cn Received 13 November 2005 revised 5 January 2006 accepted 14 February 2006 doi 10.1111 j.1742-4658.2006.05178.x The availability of the complete chicken genome sequence provides an unprecedented opportunity to study the global genome organization at the sequence level. Delineating compositionally homogeneous G C domains in DNA sequences can provide much insight into the understanding of the organization and biological functions of the chicken genome. A new segmentation algorithm which is simple and fast has been proposed to partition a given genome or DNA sequence into compositionally distinct domains. By applying the new segmentation algorithm to the draft chicken genome sequence the mosaic organization of the chicken genome can be confirmed at the sequence level. It is shown herein that the chicken genome is also characterized by a mosaic structure of isochores long DNA segments that are fairly homogeneous in the G C content. Consequently 25 isochores longer than 2 Mb megabases have been identified in the chicken genome. These isochores have a fairly homogeneous G C content and often correspond to meaningful biological units. With the aid of the technique of cumulative GC profile we proposed an intuitive picture to display the distribution of segmentation points. The relationships between G C content and the distributions of genes CpG islands and other genomic elements were analyzed in a perceivable manner. The cumulative GC profile equipped with the new segmentation algorithm would be an appropriate starting point for analyzing the isochore structures of higher eukaryotic .
