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In Silico Biology 1, 0009 (1998); ©1998, Bioinformation Systems e.V.  

Use of Contiguity on the Chromosome to Predict Functional Coupling

Ross Overbeek, Michael Fonstein*, Mark D'Souza, Gordon D. Pusch and Natalia Maltsev

Mathematics and Computer Science Division, Argonne National Laboratory, IL 60439, USA
* Department of Molecular Genetics and Cell Biology, University of Chicago, IL 60637, USA.

Edited by E. Koonin; received April 16, 1998; revised June 1, 1998; accepted June 3, 1998


The availability of a growing number of completely sequenced genomes opens new opportunities for understanding of complex biological systems. Success of genome-based biology will, to a large extent, depend on the development of new approaches and tools for efficient comparative analysis of the genomes and  their organization. We have developed a technique for detecting possible functional coupling between genes based on detection of potential operons. The approach involves computation of "pairs of close bi-directional best hits", which are pairs of genes that apparently occur within operons in multiple genomes.  Using these pairs, one can compose evidence (based on the number of distinct genomes and the phylogenetic distance between the orthologous pairs) that a pair of genes is potentially functionally coupled.  The technique has revealed a surprisingly rich and apparently accurate set of functionally coupled genes.  The approach depends on the use of a relatively large number of genomes, and the amount of detected coupling grows dramatically as the number of genomes increases.

Key words: microbial genomes, operons, gene function identification, genetic sequence analysis, comparative analysis