Bioinformatics Vol. 17 no. 9 2001
Pages 791-802
© 2001 Oxford University Press
Comprehensive comparison between locations of orthologous genes on archaeal and bacterial genomes
1 Laboratory of Mathematics, Saga Medical
School, 5-1-1 Nabeshima, Saga 849-8501, Japan
2 Center for Information Biology, National
Institute of Genetics, Yata 1111, Mishima 411-8540, Japan
3 Japan Network Information Center, 1-2
Kanda-Ogawa, Chiyoda, Tokyo 101-0052, Japan
Received on December 1, 2000
; revised on April 4, 2001
; accepted on May 7, 2001
Motivation: Following an extensive search for orthologous genes between the complete genomes from archaea and bacteria, the spatial association of the orthologs has been investigated in terms of synteny, the conservation of the order of neighboring genes. However, the relationships between the relative locations of remote orthologs over entire genomes have not been shown.
Results: Comprehensive comparisons between the locations of orthologs on nineteen archaeal and bacterial genomes are presented by the location to location correspondence based on the gene–location distance. When the two genomes are rotated such that a pair of orthologs with the shortest distance is set in the same angle, a statistically significant number of orthologs maintain their relative locations between the genomes. Even by the short distances at the 5% significance level, the rotations are restricted within a narrow range, suggesting an intrinsic angle for realizing similar locations between the orthologs in each genome pair. Furthermore, the rotations in the restricted range agree with the replication origin and terminus sites for the analyzed genomes where such sites are known. The relationship between location-maintained orthologs and gene function is also discussed.
Contact: horimoto{at}post.saga-med.ac.jp