107. Comparative Analyses of Syntenic Blocks 

Jonathan E. Moore and James A. Lake 
Molecular Biology Institute, University of California, Los Angeles, CA 90095 
Lake@mbi.ucla.edu 

The comparative analysis of syntenic blocks common to the genomes of closely related organisms, such as those found in humans and mice, appears to have enormous potential to aid in the identification of gene boundaries, open reading frames (ORFs), and the interpretation of gene organization. Recently, pattern filtering, a new genome analysis tool has been developed. Pattern filtering methods appear to be able to obtain an optimal signal to noise ratio when used to search for ORFs and also simplify the analysis of codon periodicities. In initial studies, it appears to be a sensitive and robust indicator of ORFs, and of gene structure and organization. Our major goal is to develop rapid, simple, and effective methods for analyzing syntenic blocks from human, mouse, Drosophila, and Caenorhabditis genomes using pattern filtering to optimally determine rates of evolution and thereby map ORFs, gene boundaries, regulatory regions, and introns. Preliminary experiments with syntenic blocks in human chromosome 12p13 and the corresponding region in mouse, and also experiments with mammalian mitochondrial DNAs, will be used to illustrate the potential of the method.