165. WIT System: Advantages of Parallel Analysis of Multiple Genomes 

Ross Overbeek, Mark D'Souza, Gordon Pusch, Natalia Maltsev, and Evgeni Selkov 
Argonne National Laboratory, Argonne, Illinois 
maltsev@mcs.anl.gov 

The WIT system (http://wit.mcs.anl.gov/WIT2/wit.html) was designed and implemented to support genetic sequence and comparative analysis of sequenced genomes and metabolic reconstructions from the sequence data. It now contains data from 34 distinct genomes, although a few of the genomes are quite incomplete. It provides access to thoroughly annotated genomes within a framework of metabolic reconstructions, connected to the sequence data; data on regulatory patterns, protein alignments and phylogenetic trees; as well as data on gene clusters and functional domains. We believe that the parallel analysis of a large number of phylogenetically diverse genomes simultaneously can add a great deal to our understanding of the higher level functional subsystems and major physiological designs. We recently developed a method for using conserved clusters of genes on the chromosome from numerous genomes to predict functional coupling between genes in those genomes¹. The results obtained by applying this method to analysis of 34 genomes in WIT collection were very encouraging. We were able to predict major portions of most of the pathways of central metabolism (e.g. glycolysis, purine, pyrimidine biosynthesis, signal transduction, transmembrane transport pathways, etc). Our results agree well with the functional connections between the genes previously described in the literature. We believe that the precision of prediction and the amount of accessible functional coupling increases dramatically as more genomes are included in the analysis. As the number of genomes increases, this class of data may well become one of the significant resources in the effort to establish the function of the hypothetical proteins, better understanding of the functions of the paralogous genes and reconstruction of the functional connections in the higher level functional subsystems. 

¹Ross Overbeek, Michael Fonstein, Mark D'Souza, Gordon D. Pusch and Natalia Maltsev. Use of Contiguity on the Chromosome to Predict Functional Coupling. (June, 1998) In Silico Biol. 1, 0009